def install_make():
click.secho("We need to install make ...\n", fg="red")
if platform.system() != "Windows":
call_cmd("sudo -k -H apt install make")
else:
click.fail("As a windows user, you must install `make` manually. "
"See: http://bfy.tw/NI8r")
def cli(ctx):
"""
Interface with a YubiKey via the command line.
"""
subcmd = next(c for c in COMMANDS if c.name == ctx.invoked_subcommand)
transports = getattr(subcmd, 'transports', TRANSPORT.usb_transports())
if transports:
try:
descriptors = list(get_descriptors())
except usb.core.NoBackendError:
click.fail('No PyUSB backend detected!')
n_keys = len(descriptors)
if n_keys == 0:
ctx.fail('No YubiKey detected!')
if n_keys > 1:
ctx.fail('Multiple YubiKeys detected. Only a single YubiKey at a '
'time is supported.')
descriptor = descriptors[0]
if descriptor.mode.transports & transports:
try:
ctx.obj['dev'] = descriptor.open_device(transports)
if not ctx.obj['dev']: # Key should be there, busy?
raise FailedOpeningDeviceException()
except FailedOpeningDeviceException:
ctx.fail('Failed connecting to the YubiKey. Is it in use by '
'another process?')
else:
req = ', '.join((t.name for t in TRANSPORT if t & transports))
click.echo("Command '{}' requires one of the following transports "
"to be enabled: '{}'.".format(subcmd.name, req))
ctx.fail("Use 'ykman mode' to set the enabled connections.")
def create_api_key():
""" Interactively create a new API key via Zotero's OAuth API.
Requires the user to enter a verification key displayed in the browser.
:returns: API key and the user's library ID
"""
auth = OAuth1Service(
name='zotero',
consumer_key=CLIENT_KEY,
consumer_secret=CLIENT_SECRET,
request_token_url=REQUEST_TOKEN_URL,
access_token_url=ACCESS_TOKEN_URL,
authorize_url=AUTH_URL,
base_url=BASE_URL)
token, secret = auth.get_request_token(
params={'oauth_callback': 'oob'})
auth_url = auth.get_authorize_url(token)
auth_url += '&' + urlencode({
'name': 'zotero-cli',
'library_access': 1,
'notes_access': 1,
'write_access': 1,
'all_groups': 'read'})
click.echo("Opening {} in browser, please confirm.".format(auth_url))
click.launch(auth_url)
verification = click.prompt("Enter verification code")
token_resp = auth.get_raw_access_token(
token, secret, method='POST',
data={'oauth_verifier': verification})
if not token_resp:
logging.debug(token_resp.content)
click.fail("Error during API key generation.")
access = urlparse.parse_qs(token_resp.text)
return access['oauth_token'][0], access['userID'][0]
def create_api_key():
""" Interactively create a new API key via Zotero's OAuth API.
Requires the user to enter a verification key displayed in the browser.
:returns: API key and the user's library ID
"""
auth = OAuth1Service(
name='zotero',
consumer_key=CLIENT_KEY,
consumer_secret=CLIENT_SECRET,
request_token_url=REQUEST_TOKEN_URL,
access_token_url=ACCESS_TOKEN_URL,
authorize_url=AUTH_URL,
base_url=BASE_URL)
token, secret = auth.get_request_token(
params={'oauth_callback': 'oob'})
auth_url = auth.get_authorize_url(token)
auth_url += '&' + urlencode({
'name': 'zotero-cli',
'library_access': 1,
'notes_access': 1,
'write_access': 1,
'all_groups': 'read'})
click.echo("Opening {} in browser, please confirm.".format(auth_url))
click.launch(auth_url)
verification = click.prompt("Enter verification code")
token_resp = auth.get_raw_access_token(
token, secret, method='POST',
data={'oauth_verifier': verification})
if not token_resp:
logging.debug(token_resp.content)
click.fail("Error during API key generation.")
access = urlparse.parse_qs(token_resp.text)
return access['oauth_token'][0], access['userID'][0]
def state(ctx, module, identifier, db, table, key_map, verbose, namespace):
"""
Dump the current state of the identifier for the specified module from Redis DB or CONFIG_FILE
"""
if not multi_asic.is_multi_asic() and namespace != DEFAULT_NAMESPACE:
click.echo("Namespace option is not valid for a single-ASIC device")
ctx.exit()
if multi_asic.is_multi_asic() and (namespace != DEFAULT_NAMESPACE
and namespace
not in multi_asic.get_namespace_list()):
click.echo("Namespace option is not valid. Choose one of {}".format(
multi_asic.get_namespace_list()))
ctx.exit()
if module not in plugins.dump_modules:
click.echo("No Matching Plugin has been Implemented")
ctx.exit()
if verbose:
os.environ["VERBOSE"] = "1"
else:
os.environ["VERBOSE"] = "0"
ctx.module = module
obj = plugins.dump_modules[module]()
if identifier == "all":
ids = obj.get_all_args(namespace)
else:
ids = identifier.split(",")
params = {}
collected_info = {}
params['namespace'] = namespace
for arg in ids:
params[plugins.dump_modules[module].ARG_NAME] = arg
try:
collected_info[arg] = obj.execute(params)
except ValueError as err:
click.fail(f"Failed to execute plugin: {err}")
if len(db) > 0:
collected_info = filter_out_dbs(db, collected_info)
vidtorid = extract_rid(collected_info, namespace)
if not key_map:
collected_info = populate_fv(collected_info, module, namespace)
for id in vidtorid.keys():
collected_info[id]["ASIC_DB"]["vidtorid"] = vidtorid[id]
print_dump(collected_info, table, module, identifier, key_map)
return
def get_confluence_cmd():
"""Assemble mandatory parameters for the Confluence command."""
try:
command_path = environ['CONFLUENCE_COMMAND_PATH']
except KeyError as error:
click.fail('Unable to access {}'.format(str(error)))
credentials = get_credentials()
return [
command_path, '--server', CONFLUENCE_URL, '--user',
credentials['username'], '--password', credentials['password']
]
def growth(ctx, **kwargs):
"""Attempts to compute growth rate (i.e. fit e^(2x)) from DynVector
data, typically an integrated quantity like electric or magnetic
field energy.
"""
vlog(ctx, 'Starting growth')
pushChain( ctx, 'growth', **kwargs)
data = ctx.obj['data']
for dat in data.iterator(kwargs['use']):
time = dat.getGrid()
values = dat.getValues()
numDims = dat.getNumDims()
if numDims > 1:
click.fail(click.style("'growth' is available only for 1D data (used on {:d}D data)".format(numDims), fg='red'))
#end
bestParams, bestR2, bestN = fitGrowth(time[0], values[..., 0],
minN=kwargs['minn'],
maxN=kwargs['maxn'],
p0=kwargs['guess'])
if kwargs['plot'] is True:
vlog(ctx, 'growth: Plotting data and fit')
plt.style.use(os.path.dirname(os.path.realpath(__file__)) \
+ "/../output/postgkyl.mplstyle")
fig, ax = plt.subplots()
ax.plot(time[0], values[..., 0], '.')
ax.set_autoscale_on(False)
ax.plot(time[0], exp2(time[0], *bestParams))
ax.grid(True)
plt.show()
#end
if kwargs['instantaneous'] is True:
vlog(ctx, 'growth: Plotting instantaneous growth rate')
gammas = []
for i in range(1,len(time[0])-1):
gamma = (values[i+1,0] - values[i-1,0])/(2*values[i,0]*(time[0][i+1] - time[0][i-1]))
gammas.append(gamma)
plt.style.use(os.path.dirname(os.path.realpath(__file__)) \
+ "/../output/postgkyl.mplstyle")
fig, ax = plt.subplots()
ax.plot(time[0][1:-1], gammas)
#ax.set_autoscale_on(False)
ax.grid(True)
plt.show()
#end
#end
vlog(ctx, 'Finishing growth')
def import_(bundleid):
for path, plist in alfredcli.util.workflows():
if plist.get("bundleid") == bundleid:
break
else:
click.fail("Unable to find bundle id: {0}".format(bundleid))
source_dir = os.path.dirname(path)
dest_dir = os.getcwd()
click.echo("Importing {0} from {1} to {2}".format(bundleid, source_dir, dest_dir))
for root, dirs, files in os.walk(source_dir):
for f in files:
# if f != 'info.plist':
# continue
source_path = os.path.join(root, f)
dest_path = os.path.join(dest_dir, f)
click.echo("Copying {0} to {1}".format(source_path, dest_path))
shutil.copy(source_path, dest_path)
def motion(input: hansel.Crumb, extra: pd.DataFrame, out_file: hansel.Crumb):
""" Create in `out_path` an Excel spreadsheet with some of the motion statistics obtained from the
`statistics_files` output of the nipype.RapidArt found in the hansel.Crumb `motion_file_cr`.
Examples: \n
nitap motion -i "/data/hansel/cobre/{sid}/{session}/rest/artifact_stats/motion_stats.json" -o motion.xls\n
nitap motion -i "/data/nuk/out/{group}/{sid}/session_0/rest/artifact_stats/motion_stats.json" -o motion.xls\n
"""
from neuro_pypes.fmri.utils import motion_stats_sheet
crumb_args = list(input.open_args())
df = motion_stats_sheet(input, crumb_args)
if extra:
extra_columns = set(extra.columns.values)
matched_args = extra_columns.intersection(crumb_args)
if not matched_args:
click.fail('Found no matches in the spreadsheet file between: '
'"{}" and "{}".'.format(extra_columns, crumb_args))
df.join(extra, on=matched_args)
df.to_excel(out_file)
print(
'Successfully wrote the motions spreadsheet in "{}".'.format(out_file))
def main(group_id, location, time_boundary, event_status, pandoc, force):
key_path = os.path.normpath(os.path.expanduser('~/.meetup.com-key'))
if os.path.exists(key_path):
with io.open(key_path, encoding='utf8') as fh:
key = fh.read().strip()
else:
key = None
cache = FileCache('.web_cache', forever=True)
requests = CacheControl(Session(),
cache,
cache_etags=False,
heuristic=ExpiresAfter(days=1))
while True:
resp = requests.get('https://api.meetup.com/status',
params=dict(key=key))
if resp.status_code == 200 and resp.json().get('status') == 'ok':
break
elif resp.status_code == 200 and any(
'auth_fail' == e.code for e in resp.json().get('errors', [])):
click.echo(
'Your meetup.com key is required. You can get it from https://secure.meetup.com/meetup_api/key/\n'
)
if click.confirm(
'Open https://secure.meetup.com/meetup_api/key/ in your web browser?'
):
click.launch('https://secure.meetup.com/meetup_api/key/')
click.echo('')
key = click.prompt('Key', hide_input=True)
else:
raise click.ClickException(
'Failed to get meetup.com status. Response was {!r} {!r}'.
format(resp.status_code, resp.text))
click.secho(
'For convenience your key is saved in `{}`.\n'.format(key_path),
fg='magenta')
with open(key_path, 'w') as fh:
fh.write(key)
while not location:
location = location or get_input(
u'Location: ',
completer=WordCompleter(
[u'cluj', u'iasi', u'timisoara', u'bucuresti'],
ignore_case=True))
while True:
group_id = group_id or get_input(
u'Group ID: ',
completer=WordCompleter([
u'RoPython-Bucuresti', u'RoPython-Cluj', u'RoPython_Iasi',
u'RoPython-Timisoara'
],
ignore_case=True))
resp = requests.get('https://api.meetup.com/2/events',
params=dict(
key=key,
group_urlname=group_id,
time=time_boundary,
status=event_status,
))
if resp.status_code == 200:
json = resp.json()
if json['results']:
break
else:
click.secho(
'Invalid group `{}`. It has no events!'.format(group_id),
fg='red')
group_id = None
if resp.status_code == '400':
click.fail(
'Failed to get make correct request. Response was {!r}'.format(
resp.text))
else:
click.secho('Invalid group `{}`. Response was [{}] {!r}'.format(
group_id, resp.status_code, resp.text),
fg='red')
# click.echo(pformat(dict(resp.headers)))
for event in json['results']:
dt = datetime.fromtimestamp(event['time'] / 1000)
event['duration'] = format_duration(
event.get('duration', 3600000) / 1000)
event['time'] = dt.strftime('%Y-%m-%d %H:%M')
if 'how_to_find_us' in event:
address = event['how_to_find_us'],
else:
address = ()
if 'venue' in event:
address_1 = event['venue'].get('address_1')
if address_1:
address += address_1,
event['venue']['address_1'] = ', '.join(address)
else:
event['venue'] = {'address_1': address}
click.echo("{time}: {name}".format(**event))
click.echo("\t{}".format(pformat(event)))
existing_path = glob(
os.path.join('content', '*', dt.strftime('%Y-%m-%d*'),
'index.rst'))
if existing_path and not force:
if len(existing_path) > 1:
click.secho('\tERROR: multiple paths matched: {}'.format(
existing_path))
else:
click.secho('\t`{}` already exists. Not importing.'.format(
*existing_path),
fg='yellow')
else:
target_dir = os.path.join(
'content', location, '{}-{}'.format(dt.strftime('%Y-%m-%d'),
slugify(event['name'])))
target_path = os.path.join(target_dir, 'index.rst')
if not os.path.exists(target_dir):
os.makedirs(target_dir)
if pandoc:
with tempfile.NamedTemporaryFile(delete=False) as fh:
fh.write(event['description'].encode('utf-8'))
rst = subprocess.check_output(
['pandoc', '--from=html', '--to=rst',
fh.name]).decode('utf-8')
os.unlink(fh.name)
else:
rst = html2rest(event['description'])
doc = u'''{name}
###############################################################
:tags: prezentari
:registration:
meetup.com: {event_url}
:start: {time}
:duration: {duration}
:location: {venue[address_1]}, {venue[city]}, {venue[localized_country_name]}
{rst}'''.format(rst=rst, **event)
with io.open(target_path, 'w', encoding='utf-8') as fh:
fh.write(doc)
click.secho('\tWrote `{}`.'.format(target_path), fg='green')
def main(group_id, location, time_boundary, event_status, pandoc):
key_path = os.path.normpath(os.path.expanduser('~/.meetup.com-key'))
if os.path.exists(key_path):
with open(key_path) as fh:
key = fh.read().strip()
cache = FileCache('.web_cache', forever=True)
requests = CacheControl(
Session(), cache,
cache_etags=False,
heuristic=ExpiresAfter(days=1)
)
while True:
resp = requests.get('https://api.meetup.com/status', params=dict(key=key))
if resp.status_code == 200:
break
elif resp.status_code == 401:
click.echo('Your meetup.com key is required. You can get it from https://secure.meetup.com/meetup_api/key/\n')
if click.confirm('Open https://secure.meetup.com/meetup_api/key/ in your web browser?'):
click.launch('https://secure.meetup.com/meetup_api/key/')
click.echo('')
key = click.prompt('Key', hide_input=True)
else:
click.fail('Failed to get meetup.com status. Response was {!r}'.format(resp.text))
click.secho('For convenience your key is saved in `{}`.\n'.format(key_path), fg='magenta')
with open(key_path, 'w') as fh:
fh.write(key)
while not location:
location = location or get_input('Location: ', completer=WordCompleter(['cluj', 'iasi', 'timisoara'], ignore_case=True))
while True:
group_id = group_id or get_input('Group ID: ', completer=WordCompleter(['Cluj-py', 'RoPython-Timisoara'], ignore_case=True))
resp = requests.get('https://api.meetup.com/2/events', params=dict(
key=key,
group_urlname=group_id,
time=time_boundary,
status=event_status,
))
if resp.status_code == 200:
json = resp.json()
if json['results']:
break
else:
click.secho('Invalid group `{}`. It has no events!'.format(group_id), fg='red')
group_id = None
if resp.status_code == '400':
click.fail('Failed to get make correct request. Response was {!r}'.format(resp.text))
else:
click.secho('Invalid group `{}`. Response was [{}] {!r}'.format(group_id, resp.status_code, resp.text), fg='red')
# click.echo(pformat(dict(resp.headers)))
for event in json['results']:
dt = datetime.fromtimestamp(event['time']/1000)
click.echo("{}: {}".format(
dt.strftime('%Y-%m-%d %H:%M:%S'),
event['name']
))
existing_path = glob(os.path.join('content', '*', dt.strftime('%Y-%m-%d*'), 'index.rst'))
if existing_path:
if len(existing_path) > 1:
click.secho('\tERROR: multiple paths matched: {}'.format(existing_path))
else:
click.secho('\t`{}` already exists. Not importing.'.format(*existing_path), fg='yellow')
else:
target_dir = os.path.join('content', location, '{}-{}'.format(dt.strftime('%Y-%m-%d'), slugify(event['name'])))
target_path = os.path.join(target_dir, 'index.rst')
if not os.path.exists(target_dir):
os.makedirs(target_dir)
if pandoc:
with tempfile.NamedTemporaryFile(delete=False) as fh:
fh.write(event['description'].encode('utf-8'))
rst = subprocess.check_output(['pandoc', '--from=html', '--to=rst', fh.name]).decode('utf-8')
print fh.name
#os.unlink(fh.name)
else:
stream = StringIO()
html2rest(event['description'].encode('utf-8'), writer=stream)
rst = stream.getvalue().decode('utf-8')
with io.open(target_path, 'w', encoding='utf-8') as fh:
fh.write('''{name}
###############################################################
:tags: unknown
:registration:
meetup.com: {event_url}
{rst}'''.format(rst=rst, **event))
click.secho('\tWrote `{}`.'.format(target_path), fg='green')
def standard(ct_file_name, rods_file_name, density_file_name, densities,
csv_file_name):
'''Determine the calibration equation for a standard phantom.'''
click.echo(echo_arguments('Standard Calibration', locals()))
# Read
click.echo('Reading input {}'.format(ct_file_name))
ct = sitk.ReadImage(ct_file_name)
click.echo('Reading input {}'.format(rods_file_name))
rods = sitk.ReadImage(rods_file_name)
# Determine number of components
click.echo('Determining mean intensities')
filt = sitk.LabelStatisticsImageFilter()
filt.Execute(ct, rods)
n_labels = len(filt.GetLabels())
click.echo('Found {} labels'.format(n_labels))
if len(densities) < 2:
click.fail('Need at least 2 samples to fit a function.'
' Only found {}'.format(len(densities)))
# Get the HU samples
HU = []
for label in filt.GetLabels():
# Skip background label
if label == 0:
continue
HU.append(filt.GetMean(label))
click.echo('Fitting parameters:')
click.echo(' Densities: {}'.format(densities))
click.echo(' HU: {}'.format(HU))
# Perform calibration
calibrator = StandardCalibration()
calibrator.fit(HU, densities)
click.echo('Found fit:')
click.echo(' Slope: {}'.format(calibrator.slope))
click.echo(' Intercept: {}'.format(calibrator.intercept))
click.echo(' R^2: {}'.format(calibrator.r_value**2))
header = [
'CT File Name', 'Rods File Name', 'Density File Name', 'slope',
'intercept', 'r_value', 'p_value', 'std_err'
]
data = {
'CT File Name': ct_file_name,
'Rods File Name': rods_file_name,
'Density File Name': density_file_name,
'slope': round(calibrator.slope, 16),
'intercept': round(calibrator.intercept, 16),
'r_value': round(calibrator.r_value, 16),
'p_value': round(calibrator.p_value, 16),
'std_err': round(calibrator.std_err, 16)
}
click.echo('Writing complete results to {}'.format(csv_file_name))
write_csv(data, csv_file_name, header)
click.echo('Calibrating density file')
density = calibrator.slope * sitk.Cast(ct, sitk.sitkFloat32) + \
calibrator.intercept
click.echo('Writing density file to {}'.format(density_file_name))
sitk.ReadImage(density, density_file_name)
def mindways(ct_file_name, rods_file_name, density_file_name, csv_file_name,
water, densities):
'''Determine the calibration equation for a Mindways phantom.
Water and K2HPO4 densities are taken from the QC documentation
accompanying your specific phantom.'''
click.echo(echo_arguments('Mindways Calibration', locals()))
# Read
click.echo('Reading input {}'.format(ct_file_name))
ct = sitk.ReadImage(ct_file_name)
click.echo('Reading input {}'.format(rods_file_name))
rods = sitk.ReadImage(rods_file_name)
# Determine number of components
click.echo('Determining mean intensities')
filt = sitk.LabelStatisticsImageFilter()
filt.Execute(ct, rods)
n_labels = len(filt.GetLabels())
click.echo('Found {} labels'.format(n_labels))
if len(water) != len(densities) or len(water) != n_labels - 1:
click.fail(
'Number of water, K2HPO4, and segmented labels are not the same '
'({}, {}, and {})'.format(len(water), len(densities),
n_labels - 1))
if len(water) < 2:
click.fail('Need at least 2 samples to fit a function.'
' Only found {}'.format(len(water)))
# Get the HU samples
HU = []
for label in filt.GetLabels():
# Skip background label
if label == 0:
continue
HU.append(filt.GetMean(label))
click.echo('Fitting parameters:')
click.echo(' Water: {}'.format(water))
click.echo(' K2HPO4: {}'.format(densities))
click.echo(' HU: {}'.format(HU))
# Perform calibration
calibrator = MindwaysCalibration()
calibrator.fit(HU, densities, water)
click.echo('Found fit:')
click.echo(' Slope: {}'.format(calibrator.slope))
click.echo(' Intercept: {}'.format(calibrator.intercept))
click.echo(' R^2: {}'.format(calibrator.r_value**2))
header = [
'CT File Name', 'Rods File Name', 'Density File Name', 'sigma_ref',
'beta_ref', 'sigma_ct', 'beta_ct', 'slope', 'intercept', 'r_value',
'p_value', 'std_err'
]
data = {
'CT File Name': ct_file_name,
'Rods File Name': rods_file_name,
'Density File Name': density_file_name,
'sigma_ref': round(calibrator.sigma_ref, 16),
'beta_ref': round(calibrator.beta_ref, 16),
'sigma_ct': round(calibrator.sigma_ct, 16),
'beta_ct': round(calibrator.beta_ct, 16),
'slope': round(calibrator.slope, 16),
'intercept': round(calibrator.intercept, 16),
'r_value': round(calibrator.r_value, 16),
'p_value': round(calibrator.p_value, 16),
'std_err': round(calibrator.std_err, 16)
}
click.echo('Writing complete results to {}'.format(csv_file_name))
write_csv(data, csv_file_name, header)
click.echo('Calibrating density file')
density = calibrator.slope * sitk.Cast(ct, sitk.sitkFloat32) + \
calibrator.intercept
click.echo('Writing density file to {}'.format(density_file_name))
sitk.ReadImage(density, density_file_name)
