def check_version(cluster):
"""Check the gluster version, exit if less than 3.12"""
if version(cluster.glusterfs_version) < version(supported_version):
print("gstatus: GlusterFS %s is not supported, use GlusterFS %s "
"or above." % (glusterfs_version, supported_version),
file=sys.stderr)
exit(1)
def __init__(self, ppm=0, osr=4, fc=940e6, samp_rate_in=1e6):
grgsm.hier_block.__init__(
self,
"GSM input adaptor",
gr.io_signature(1, 1, gr.sizeof_gr_complex * 1),
gr.io_signature(1, 1, gr.sizeof_gr_complex * 1),
)
##################################################
# Parameters
##################################################
self.ppm = ppm
self.osr = osr
self.fc = fc
self.samp_rate_in = samp_rate_in
##################################################
# Variables
##################################################
self.samp_rate_out = samp_rate_out = 1625000.0 / 6.0 * osr
##################################################
# Blocks
##################################################
if version(gr.version()) >= version('3.7.9'):
self.message_port_register_hier_in("ppm_in")
else:
self.message_port_register_hier_out("ppm_in")
self.low_pass_filter_0_0 = filter.fir_filter_ccf(
1,
firdes.low_pass(1, samp_rate_out, 125e3, 5e3, firdes.WIN_HAMMING,
6.76))
self.gsm_clock_offset_corrector_0 = grgsm.clock_offset_corrector(
fc=fc,
ppm=ppm,
samp_rate_in=samp_rate_in,
)
self.fractional_resampler_xx_0 = filter.fractional_resampler_cc(
0, samp_rate_in / samp_rate_out)
##################################################
# Connections
##################################################
self.connect((self.low_pass_filter_0_0, 0), (self, 0))
self.connect((self.fractional_resampler_xx_0, 0),
(self.low_pass_filter_0_0, 0))
self.connect((self.gsm_clock_offset_corrector_0, 0),
(self.fractional_resampler_xx_0, 0))
self.connect((self, 0), (self.gsm_clock_offset_corrector_0, 0))
##################################################
# Asynch Message Connections
##################################################
self.msg_connect(self, "ppm_in", self.gsm_clock_offset_corrector_0,
"ppm_in")
def version_check():
if version(URLLIB3_VERSION) >= version(URLLIB3_MIN_REQUIRED_VERSION):
return
err = '{0} version: {1}, minimum required version: {2}, please upgrade'.format(
URLLIB3,
URLLIB3_VERSION,
URLLIB3_MIN_REQUIRED_VERSION,
)
raise Exception(err)
class DeltaDiracModel(Model):
r"""A function that is zero everywhere except for the x-value closest
to the center parameter.
At value-closest-to-center, the model evaluates to the amplitude
parameter divided by the x-spacing. This last division is
necessary to preserve normalization with integrating the function
over the X-axis
Fitting parameters:
- integrated intensity ``amplitude`` :math:`A`
- position of the peak ``center`` :math:`E_0`
"""
def __init__(self,
independent_vars=['x'],
prefix='',
missing=None,
name=None,
**kwargs):
kwargs.update({
'prefix': prefix,
'missing': missing,
'independent_vars': independent_vars
})
super(DeltaDiracModel, self).__init__(delta_dirac, **kwargs)
if version(lmfit.__version__) > version('0.9.5'):
__init__.__doc__ = lmfit.models.COMMON_INIT_DOC
def guess(self, y, x=None, **kwargs):
r"""Guess starting values for the parameters of a model.
Parameters
----------
y : :class:`~numpy:numpy.ndarray`
Intensities
x : :class:`~numpy:numpy.ndarray`
energy values
kwargs : dict
additional optional arguments, passed to model function.
Returns
-------
:class:`~lmfit.parameter.Parameters`
parameters with guessed values
"""
amplitude = max(y)
center = 0.0
if x is not None:
center = x[index_of(y, max(y))]
dx = (x[-1] - x[0]) / (len(x) - 1) # x-spacing
amplitude /= dx
return self.make_params(amplitude=amplitude, center=center)
def get_from_api(uri):
"""
Get an object from the api
"""
headers = {'Accept': 'application/json'}
r = requests.get(APIURI+uri+"?limit="+APILIMIT,headers=headers)
if r.status_code != 200:
print ("Could not get "+APIURI+uri)
r.raise_for_status()
if version(requests.__version__) >= version("2.0.0"):
return r.json()
else:
return r.json
def get_from_api(uri):
"""
Get an object from the api
"""
headers = {'Accept': 'application/json'}
r = requests.get(APIURI + uri + "?limit=" + APILIMIT, headers=headers)
if r.status_code != 200:
print("Could not get " + APIURI + uri)
r.raise_for_status()
if version(requests.__version__) >= version("2.0.0"):
return r.json()
else:
return r.json
def load(self):
self.base.conf.read()
self.base.conf.cacheonly = True
self.base.read_all_repos()
self.packages = hawkey.Query(hawkey.Sack())
if version(dnf.VERSION) >= version("4.7.0"):
try:
# do not use standard self.base.fill_sack() it does not respect cacheonly
self.base.fill_sack_from_repos_in_cache(load_system_repo=True)
self.packages = self.base.sack.query()
except dnf.exceptions.RepoError:
# RepoError is raised when cache is empty
pass
self.repos = self.base.repos
def __init__(self, ppm=0, osr=4, fc=940e6, samp_rate_in=1e6):
gr.hier_block2.__init__(
self, "GSM input adaptor",
gr.io_signature(1, 1, gr.sizeof_gr_complex*1),
gr.io_signature(1, 1, gr.sizeof_gr_complex*1),
)
##################################################
# Parameters
##################################################
self.ppm = ppm
self.osr = osr
self.fc = fc
self.samp_rate_in = samp_rate_in
##################################################
# Variables
##################################################
self.samp_rate_out = samp_rate_out = 1625000.0/6.0*osr
##################################################
# Blocks
##################################################
if version(gr.version()) >= version('3.7.9'):
self.message_port_register_hier_in("ppm_in")
else:
self.message_port_register_hier_out("ppm_in")
self.low_pass_filter_0_0 = filter.fir_filter_ccf(1, firdes.low_pass(
1, samp_rate_out, 125e3, 5e3, firdes.WIN_HAMMING, 6.76))
self.gsm_clock_offset_corrector_0 = grgsm.clock_offset_corrector(
fc=fc,
ppm=ppm,
samp_rate_in=samp_rate_in,
)
self.fractional_resampler_xx_0 = filter.fractional_resampler_cc(0, samp_rate_in/samp_rate_out)
##################################################
# Connections
##################################################
self.connect((self.low_pass_filter_0_0, 0), (self, 0))
self.connect((self.fractional_resampler_xx_0, 0), (self.low_pass_filter_0_0, 0))
self.connect((self.gsm_clock_offset_corrector_0, 0), (self.fractional_resampler_xx_0, 0))
self.connect((self, 0), (self.gsm_clock_offset_corrector_0, 0))
##################################################
# Asynch Message Connections
##################################################
self.msg_connect(self, "ppm_in", self.gsm_clock_offset_corrector_0, "ppm_in")
def __init__(self, fc=936.6e6, ppm=0, samp_rate_in=1625000.0/6.0*4.0):
gr.hier_block2.__init__(
self, "Clock offset corrector",
gr.io_signature(1, 1, gr.sizeof_gr_complex*1),
gr.io_signature(1, 1, gr.sizeof_gr_complex*1),
)
if version(gr.version()) >= version('3.7.9'):
self.message_port_register_hier_in("ppm_in")
else:
self.message_port_register_hier_out("ppm_in")
##################################################
# Parameters
##################################################
self.fc = fc
self.ppm = ppm
self.samp_rate_in = samp_rate_in
##################################################
# Variables
##################################################
self.samp_rate_out = samp_rate_out = samp_rate_in
##################################################
# Blocks
##################################################
self.gsm_controlled_rotator_cc_0 = grgsm.controlled_rotator_cc(0,samp_rate_out)
self.gsm_controlled_const_source_f_0 = grgsm.controlled_const_source_f(ppm)
self.fractional_resampler_xx_0 = filter.fractional_resampler_cc(0, samp_rate_in/samp_rate_out)
self.blocks_multiply_const_vxx_0_0 = blocks.multiply_const_vff((1.0e-6*samp_rate_in/samp_rate_out, ))
self.blocks_multiply_const_vxx_0 = blocks.multiply_const_vff((fc/samp_rate_out*(2*math.pi)/1e6, ))
self.blocks_add_const_vxx_0 = blocks.add_const_vff((samp_rate_in/samp_rate_out, ))
##################################################
# Connections
##################################################
self.connect((self, 0), (self.fractional_resampler_xx_0, 0))
self.connect((self.fractional_resampler_xx_0, 0), (self.gsm_controlled_rotator_cc_0, 0))
self.connect((self.blocks_add_const_vxx_0, 0), (self.fractional_resampler_xx_0, 1))
self.connect((self.blocks_multiply_const_vxx_0_0, 0), (self.blocks_add_const_vxx_0, 0))
self.connect((self.blocks_multiply_const_vxx_0, 0), (self.gsm_controlled_rotator_cc_0, 1))
self.connect((self.gsm_controlled_rotator_cc_0, 0), (self, 0))
self.connect((self.gsm_controlled_const_source_f_0, 0), (self.blocks_multiply_const_vxx_0_0, 0))
self.connect((self.gsm_controlled_const_source_f_0, 0), (self.blocks_multiply_const_vxx_0, 0))
##################################################
# Asynch Message Connections
##################################################
self.msg_connect(self, "ppm_in", self.gsm_controlled_const_source_f_0, "constant_msg")
def label_particles_edge(im, sigma=2, closing_size=0, **extra_args):
""" label_particles_edge(image, sigma=3, closing_size=3)
Returns the labels for an image.
Segments using Canny edge-finding filter.
keyword arguments:
image -- The image in which to find particles
sigma -- The size of the Canny filter
closing_size -- The size of the closing filter
"""
from skimage.morphology import square, binary_closing, skeletonize
if skversion < version('0.11'):
from skimage.filter import canny
else:
from skimage.filters import canny
edges = canny(im, sigma=sigma)
if closing_size > 0:
edges = binary_closing(edges, square(closing_size))
edges = skeletonize(edges)
labels = sklabel(edges)
print "found {} segments".format(labels.max())
labels = np.ma.array(
labels,
mask=edges == 0) # in ma.array mask, False is True, and vice versa
return labels
def dump_exception_info(exc, pages, cmdhist, objects):
"""Dump exception info to stderr.
Args:
exc: An exception tuple (type, value, traceback)
pages: A list of lists of the open pages (URLs as strings)
cmdhist: A list with the command history (as strings)
objects: A list of all QObjects as string.
"""
print(file=sys.stderr)
print("\n\n===== Handling exception with --no-err-windows... =====\n\n",
file=sys.stderr)
print("\n---- Exceptions ----", file=sys.stderr)
print(''.join(traceback.format_exception(*exc)), file=sys.stderr)
print("\n---- Version info ----", file=sys.stderr)
try:
print(version.version(), file=sys.stderr)
except Exception:
traceback.print_exc()
print("\n---- Config ----", file=sys.stderr)
try:
conf = objreg.get('config')
print(conf.dump_userconfig(), file=sys.stderr)
except Exception:
traceback.print_exc()
print("\n---- Commandline args ----", file=sys.stderr)
print(' '.join(sys.argv[1:]), file=sys.stderr)
print("\n---- Open pages ----", file=sys.stderr)
print('\n\n'.join('\n'.join(e) for e in pages), file=sys.stderr)
print("\n---- Command history ----", file=sys.stderr)
print('\n'.join(cmdhist), file=sys.stderr)
print("\n---- Objects ----", file=sys.stderr)
print(objects, file=sys.stderr)
def filter_segments(labels, max_ecc, min_area, max_area, max_detect=None,
circ=None, intensity=None, **extra_args):
""" filter_segments(labels, max_ecc=0.5, min_area=15, max_area=200) -> [Segment]
Returns a list of Particles and masks out labels for
particles not meeting acceptance criteria.
"""
pts = []
strengths = []
centroid = 'Centroid' if intensity is None else 'WeightedCentroid'
if skversion < version('0.10'):
rprops = regionprops(labels, ['Area', 'Eccentricity', centroid], intensity)
else:
rprops = regionprops(labels, intensity)
for rprop in rprops:
area = rprop['area']
if area < min_area or area > max_area:
continue
ecc = rprop['eccentricity']
if ecc > max_ecc:
continue
x, y = rprop[centroid]
if circ:
co, ro = circ
if (x - co[0])**2 + (y - co[1])**2 > ro**2:
continue
pts.append(Segment(x, y, rprop.label, ecc, area))
if max_detect is not None:
strengths.append(rprop['mean_intensity'])
if max_detect is not None:
pts = pts[np.argsort(-strengths)]
return pts[:max_detect]
def run(self):
# ask or get password from command line
self.pwd = self.args.password if self.args.password else getpass()
self.sock = self.connect()
# get Odoo version:
odoo_version = self.get_odoo_version()
if version(odoo_version) >= '6.0' and version(odoo_version) < '7.0':
self.move_using_document_storage()
elif version(odoo_version) >= '7.0':
self.move_using_config_parameter()
else:
msg = ("Moving attachments in Odoo version '{}' is not yet "
"implemented").format(odoo_version)
raise Exception(msg)
def compare_version(version_left="", version_right=""):
"""
get latest version in version_lest and version right, using "from distutils.version import LooseVersion".
Refers: https://segmentfault.com/q/1010000000331434
:param version_left:
:param version_right:
:return latest version in version_lest and version right:
"""
from distutils.version import LooseVersion as version
res = cmp(version(version_left), version(version_right))
if res > 0:
return version_left
elif res < 0:
return version_right
else:
return version_left
def compare_version(version_left="", version_right=""):
"""
get latest version in version_lest and version right, using "from distutils.version import LooseVersion".
Refers: https://segmentfault.com/q/1010000000331434
:param version_left:
:param version_right:
:return latest version in version_lest and version right:
"""
from distutils.version import LooseVersion as version
res = cmp(version(version_left), version(version_right))
if res > 0:
return version_left
elif res < 0:
return version_right
else:
return version_left
def __init__(self, api_client: ApiClient) -> None:
if client_version < version('0.2.2'):
sys.exit(
'Requires carbon3d-client version of at least 0.2.2, ({v} found)'
.format(v=client_version) +
'\nUpdate with: pip install --upgrade carbon3d-client')
self.printed_parts_api = PrintedPartsApi(api_client)
self.prints_api = PrintsApi(api_client)
def open_database():
"""Open the database for editing values."""
sudo_required()
global conn
global c
# Check if Datebase is already open, else open it.
try:
conn.execute("")
except:
verbose_output("Opening Database...")
try:
if not os.path.isfile(tcc_db):
print("TCC Database has not been found.")
sys.exit(1)
conn = sqlite3.connect(tcc_db)
c = conn.cursor()
# Do a sanity check that TCC access table has expected structure
c.execute(
"SELECT sql FROM sqlite_master WHERE name='access' and type='table'"
)
accessTableDigest = ""
for row in c.fetchall():
accessTableDigest = hashlib.sha1(row[0]).hexdigest()[0:10]
break
# check if table in DB has expected structure:
if not (accessTableDigest == "8e93d38f7c" # prior to El Capitan
or (osx_version >= version(
'10.11') # El Capitan , Sierra, High Sierra
and accessTableDigest in ["9b2ea61b30", "1072dc0e4b"]) or
(osx_version >= version('10.14') # Mojave and Catalina
and accessTableDigest in ["ecc443615f", "80a4bb6912"]) or
(osx_version >= version('10.16') # Big Sur and later
and accessTableDigest == "3d1c2a0e97")):
print("TCC Database structure is unknown.")
sys.exit(1)
verbose_output("Database opened.\n")
except:
print(
"Error opening Database. You probably need to disable SIP for this to work."
)
sys.exit(1)
def disable(client):
"""Disable a client in the database."""
open_database()
verbose_output("Disabling %s..." % (client,))
# Setting typically appears in System Preferences
# right away (without closing the window).
# Set to 0 to disable the client.
enable_mode_name = 'auth_value' if osx_version >= version('10.16') else 'allowed'
c.execute("UPDATE access SET %s='0' WHERE client='%s' AND service IS '%s'" % (enable_mode_name, client, service))
commit_changes()
def insert_client(client):
#------------------------
open_database()
# Check if it is a command line utility or a bundle ID as the default value to enable it is different.
cli_util_or_bundle_id(client)
verbose_output("Inserting \"%s\" into Database..." % (client))
if osx_version >= version('10.11'): # El Capitan or higher.
c.execute("INSERT or REPLACE INTO access VALUES('kTCCServiceAccessibility','%s',%s,1,1,NULL,NULL)" % (client, client_type))
else: # Yosemite or lower.
c.execute("INSERT or REPLACE INTO access VALUES('kTCCServiceAccessibility','%s',%s,1,1,NULL)" % (client, client_type))
commit_changes()
def insert_client(client):
#------------------------
open_database()
# Check if it is a command line utility or a bundle ID as the default value to enable it is different.
cli_util_or_bundle_id(client)
verbose_output("Inserting \"%s\" into Database..." % (client))
if osx_version >= version('10.11'): # El Capitan or higher.
c.execute("INSERT or REPLACE INTO access VALUES('kTCCServiceAccessibility','%s',%s,1,1,NULL,NULL)" % (client, client_type))
else: # Yosemite or lower.
c.execute("INSERT or REPLACE INTO access VALUES('kTCCServiceAccessibility','%s',%s,1,1,NULL)" % (client, client_type))
commit_changes()
def insert_client(client):
"""Insert a client into the database."""
open_database()
# Check if it is a command line utility or a bundle ID
# as the default value to enable it is different.
cli_util_or_bundle_id(client)
verbose_output("Inserting \"%s\" into Database..." % (client))
if osx_version >= version('10.15'): # Catalina and later
c.execute("INSERT or REPLACE INTO \
access VALUES('kTCCServiceAccessibility','%s',%s,1,1,NULL,NULL,NULL,'UNUSED',NULL,0,NULL)"
% (client, client_type))
elif osx_version >= version('10.11'): # El Capitan through Mojave
c.execute("INSERT or REPLACE INTO \
access VALUES('kTCCServiceAccessibility','%s',%s,1,1,NULL,NULL)" %
(client, client_type))
else: # Yosemite or lower.
c.execute("INSERT or REPLACE INTO \
access VALUES('kTCCServiceAccessibility','%s',%s,1,1,NULL)" %
(client, client_type))
commit_changes()
def _check_xen_version(xversion, **kwargs):
log_str = 'Checking xen version: '
if xversion in XEN_VERSIONS['Custom']:
log_str += 'xen version \'{0}\' found in Custom-versions, OK'.format(xversion)
log.info(log_str)
return True
for cversion in XEN_VERSIONS['Main']:
if version(xversion) >= version(cversion):
log_str += 'xen version \'{0}\' >= \'{1}\', OK!'.format(xversion, cversion)
log.info(log_str)
return True
msg = (
'\'{0}\' not found in Xen-custom-versions '
'and {0} < Xen-Main-versions, FAILED!'
)
log_str += msg.format(xversion)
log.info(log_str)
return False
def _check_kernel_version(wversion, distro):
'''
Check current kernel version against known good versions
from distro list and custom kernel names.
'''
log_str = 'Checking kernel version: '
safe_kernels = KERNEL_VERSIONS[distro]
cust_kernels = KERNEL_VERSIONS['Custom']
# Steps:
# 1. Check excact versions in KERNEL_VERSIONS['distro']
# 2. Check excact versions in KERNEL_VERSIONS['Custom']
# 3. Compare version to known safe mainline and LTS versions
# 4. Fail if none of the above succeeded
if wversion in safe_kernels:
log_str += '\'{0}\' found in {0}-kernels, OK'.format(wversion, distro)
log.info(log_str)
return True
elif wversion in cust_kernels:
log_str += '\'{0}\' found in Custom-kernels, OK'.format(wversion, distro)
log.info(log_str)
return True
else:
for ml_version in KERNEL_VERSIONS['Mainline']:
if version(wversion) >= version(ml_version):
log_str += '\'{0}\' >= \'{1}\' from Mainline/LTS, OK!'.format(wversion, ml_version)
log.info(log_str)
return True
log_str += '\'{0}\' < \'{1}\' and its not in {2}- or Custom-kernel list, FAILED'.format(
wversion,
KERNEL_VERSIONS['Mainline'],
distro
)
log.info(log_str)
return False
def _check_bios_version(wversion, **kwargs):
log_str = 'Checking bios version: '
# create shortcut to platform data
cdata = BIOS_VERSIONS[kwargs['system_product_name']]
if not cdata['bios_version']:
msg = 'Cant check bios, no data for platform {0} available, FAILED!'
log.error(msg.format(kwargs['system_product_name']))
return False
if not wversion:
log_str += 'Bios version from system \'{0}\' unusable, Failed!'.format(wversion)
log.info(log_str)
return False
if version(wversion) > version(cdata['bios_version']):
log_str += '\'{0}\' >= \'{1}\', OK!'.format(wversion, cdata['bios_version'])
log.info(log_str)
return True
else:
log_str += '\'{0}\' < \'{1}\', FAILED!'.format(wversion, cdata['bios_version'])
log.info(log_str)
return False
def _gather_crash_info(self):
"""Gather crash information to display.
Args:
pages: A list of lists of the open pages (URLs as strings)
cmdhist: A list with the command history (as strings)
exc: An exception tuple (type, value, traceback)
"""
try:
self._crash_info.append(("Version info", version.version()))
except Exception:
self._crash_info.append(("Version info", traceback.format_exc()))
try:
conf = objreg.get('config')
self._crash_info.append(("Config", conf.dump_userconfig()))
except Exception:
self._crash_info.append(("Config", traceback.format_exc()))
def _gather_crash_info(self):
"""Gather crash information to display.
Args:
pages: A list of lists of the open pages (URLs as strings)
cmdhist: A list with the command history (as strings)
exc: An exception tuple (type, value, traceback)
"""
try:
self._crash_info.append(("Version info", version.version()))
except Exception:
self._crash_info.append(("Version info", traceback.format_exc()))
try:
conf = objreg.get('config')
self._crash_info.append(("Config", conf.dump_userconfig()))
except Exception:
self._crash_info.append(("Config", traceback.format_exc()))
def filter_segments(labels,
max_ecc,
min_area,
max_area,
max_detect=None,
circ=None,
intensity=None,
**extra_args):
""" filter_segments(labels, max_ecc=0.5, min_area=15, max_area=200) -> [Segment]
Returns a list of Particles and masks out labels for
particles not meeting acceptance criteria.
"""
pts = []
strengths = []
centroid = 'Centroid' if intensity is None else 'WeightedCentroid'
if skversion < version('0.10'):
rprops = regionprops(labels, ['Area', 'Eccentricity', centroid],
intensity)
else:
rprops = regionprops(labels, intensity)
for rprop in rprops:
area = rprop['area']
ecc = rprop['eccentricity']
if area < min_area:
#print 'too small:', area
continue
elif area > max_area:
#print 'too big:', area
continue
elif ecc > max_ecc:
#print 'too eccentric:', ecc
#labels[labels==rprop.label] = np.ma.masked
continue
x, y = rprop[centroid]
if circ:
co, ro = circ
if (x - co[0])**2 + (y - co[1])**2 > ro**2:
continue
pts.append(Segment(x, y, rprop.label, ecc, area))
if max_detect is not None:
strengths.append(rprop['mean_intensity'])
if max_detect is not None:
pts = pts[np.argsort(-strengths)]
return pts[:max_detect]
def open_database():
#------------------------
sudo_required()
global conn
global c
# Check if Datebase is already open, else open it.
try:
conn.execute("")
except:
verbose_output("Opening Database...")
try:
if not os.path.isfile(tcc_db):
print "TCC Database has not been found."
sys.exit(1)
conn = sqlite3.connect(tcc_db)
c = conn.cursor()
# Do a sanity check that TCC access table has expected structure
c.execute(
"SELECT sql FROM sqlite_master WHERE name='access' and type='table'"
)
accessTableDigest = ""
for row in c.fetchall():
accessTableDigest = hashlib.sha1(row[0]).hexdigest()[0:10]
break
# check if table in DB has expected structure:
if not (accessTableDigest == "8e93d38f7c" #prior to El Capitan
or
(osx_version >= version('10.11')
and accessTableDigest in ["9b2ea61b30", "1072dc0e4b"])):
print "TCC Database structure is unknown."
sys.exit(1)
verbose_output("Database opened.\n")
except:
print "Error opening Database."
sys.exit(1)
def label_particles_edge(im, sigma=2, closing_size=0, **extra_args):
""" label_particles_edge(image, sigma=3, closing_size=3)
Returns the labels for an image.
Segments using Canny edge-finding filter.
keyword arguments:
image -- The image in which to find particles
sigma -- The size of the Canny filter
closing_size -- The size of the closing filter
"""
from skimage.morphology import square, binary_closing, skeletonize
if skversion < version('0.11'):
from skimage.filter import canny
else:
from skimage.filters import canny
edges = canny(im, sigma=sigma)
if closing_size > 0:
edges = binary_closing(edges, square(closing_size))
edges = skeletonize(edges)
labels = sklabel(edges)
print "found {} segments".format(labels.max())
labels = np.ma.array(labels, mask=edges==0) # in ma.array mask, False is True, and vice versa
return labels
def open_database():
#------------------------
sudo_required()
global conn
global c
# Check if Datebase is already open, else open it.
try: conn.execute("")
except:
verbose_output("Opening Database...")
try:
if not os.path.isfile(tcc_db):
print "TCC Database has not been found."
sys.exit(1)
conn = sqlite3.connect(tcc_db)
c = conn.cursor()
# Do a sanity check that TCC access table has expected structure
c.execute("SELECT sql FROM sqlite_master WHERE name='access' and type='table'")
accessTableDigest=""
for row in c.fetchall():
accessTableDigest=hashlib.sha1(row[0]).hexdigest()[0:10]
break;
# check if table in DB has expected structure:
if not (
accessTableDigest == "8e93d38f7c" #prior to El Capitan
or
(osx_version >= version('10.11') and accessTableDigest in ["9b2ea61b30", "1072dc0e4b"])
):
print "TCC Database structure is unknown."
sys.exit(1)
verbose_output("Database opened.\n")
except:
print "Error opening Database."
sys.exit(1)
def filter_segments(labels, max_ecc, min_area, max_area, max_detect=None, circ=None, intensity=None, **extra_args):
""" filter_segments(labels, max_ecc=0.5, min_area=15, max_area=200) -> [Segment]
Returns a list of Particles and masks out labels for
particles not meeting acceptance criteria.
"""
pts = []
strengths = []
centroid = "Centroid" if intensity is None else "WeightedCentroid"
if skversion < version("0.10"):
rprops = regionprops(labels, ["Area", "Eccentricity", centroid], intensity)
else:
rprops = regionprops(labels, intensity)
for rprop in rprops:
area = rprop["area"]
ecc = rprop["eccentricity"]
if area < min_area:
# print 'too small:', area
continue
elif area > max_area:
# print 'too big:', area
continue
elif ecc > max_ecc:
# print 'too eccentric:', ecc
# labels[labels==rprop.label] = np.ma.masked
continue
x, y = rprop[centroid]
if circ:
co, ro = circ
if (x - co[0]) ** 2 + (y - co[1]) ** 2 > ro ** 2:
continue
pts.append(Segment(x, y, rprop.label, ecc, area))
if max_detect is not None:
strengths.append(rprop["mean_intensity"])
if max_detect is not None:
pts = pts[np.argsort(-strengths)]
return pts[:max_detect]
def message_port_register_hier_out(self, port_id):
if version(gr.version()) >= version('3.7.9'):
super(hier_block, self).message_port_register_hier_out(port_id)
else:
super(hier_block, self).message_port_register_hier_in(port_id)
#!/usr/bin/env python
from socket import gethostname
hostname = gethostname()
from distutils.version import StrictVersion as version
import skimage
skversion = version(skimage.__version__)
import numpy as np
from scipy.ndimage import gaussian_filter, median_filter, binary_erosion, convolve, center_of_mass, imread
from skimage import segmentation
if skversion < version("0.10"):
from skimage.morphology import label as sklabel
from skimage.measure import regionprops
else:
from skimage.measure import regionprops, label as sklabel
from skimage.morphology import disk as _disk
from collections import namedtuple
def label_particles_edge(im, sigma=2, closing_size=0, **extra_args):
""" label_particles_edge(image, sigma=3, closing_size=3)
Returns the labels for an image.
Segments using Canny edge-finding filter.
keyword arguments:
image -- The image in which to find particles
import sqlite3 import sys import getopt import os from platform import mac_ver from distutils.version import StrictVersion as version ############################## ######## VARIABLES ########### # Utility Name util_name = os.path.basename(sys.argv[0]) # Current OS X version osx_version = version(mac_ver()[0]) # Database Path tcc_db = '/Library/Application Support/com.apple.TCC/TCC.db' # Set "sudo" to True if called with admin-privileges. sudo = True if os.getuid() == 0 else False # Default Verbosity verbose = False ############################## ######## FUNCTIONS ########### def usage(error_code=None):
#!/usr/bin/env python
from socket import gethostname
hostname = gethostname()
from distutils.version import StrictVersion as version
import skimage
skversion = version(skimage.__version__)
import numpy as np
from scipy.ndimage import gaussian_filter, median_filter, binary_erosion, convolve, center_of_mass, imread
from skimage import segmentation
if skversion < version('0.10'):
from skimage.morphology import label as sklabel
from skimage.measure import regionprops
else:
from skimage.measure import regionprops, label as sklabel
from skimage.morphology import disk as _disk
from collections import namedtuple
def label_particles_edge(im, sigma=2, closing_size=0, **extra_args):
""" label_particles_edge(image, sigma=3, closing_size=3)
Returns the labels for an image.
Segments using Canny edge-finding filter.
keyword arguments:
image -- The image in which to find particles
sigma -- The size of the Canny filter
closing_size -- The size of the closing filter
"""
from skimage.morphology import square, binary_closing, skeletonize
import argparse import sqlite3 import sys import os import hashlib from platform import mac_ver from distutils.version import StrictVersion as version # Utility Name util_name = os.path.basename(sys.argv[0]) # Utility Version util_version = '1.2.10' # Current OS X version osx_version = version(mac_ver()[0]) # mac_ver() returns 10.16 for Big Sur instead 11.+ # Database Path tcc_db = '/Library/Application Support/com.apple.TCC/TCC.db' # Set "sudo" to True if called with Admin-Privileges. sudo = True if os.getuid() == 0 else False # Default Verbosity verbose = False # TCC Service service = "kTCCServiceAccessibility" parser = argparse.ArgumentParser(description='Modify Accesibility Preferences')
def message_port_register_hier_in(self, port_id):
if version(gr.version()) >= version('3.7.9'):
super(hier_block, self).message_port_register_hier_in(port_id)
else:
super(hier_block, self).message_port_register_hier_out(port_id)
import argparse
import sqlite3
import sys
import os
import hashlib
from platform import mac_ver
from distutils.version import StrictVersion as version
# Utility Name
util_name = os.path.basename(sys.argv[0])
# Utility Version
util_version = '1.2.5'
# Current OS X version
osx_version = version(mac_ver()[0])
# Database Path
tcc_db = '/Library/Application Support/com.apple.TCC/TCC.db'
# Set "sudo" to True if called with Admin-Privileges.
sudo = True if os.getuid() == 0 else False
# Default Verbosity
verbose = False
parser = argparse.ArgumentParser(description='Modify Accesibility Preferences')
parser.add_argument(
'action',
metavar='ACTION',
type=str,
#!/usr/bin/env python
from socket import gethostname
hostname = gethostname()
from distutils.version import StrictVersion as version
import skimage
skversion = version(skimage.__version__)
import numpy as np
from scipy.ndimage import gaussian_filter, median_filter, binary_erosion, convolve, center_of_mass, imread
from skimage import segmentation
if skversion < version('0.10'):
from skimage.morphology import label as sklabel
from skimage.measure import regionprops
else:
from skimage.measure import regionprops, label as sklabel
from skimage.morphology import disk as _disk
from collections import namedtuple
def label_particles_edge(im, sigma=2, closing_size=0, **extra_args):
""" label_particles_edge(image, sigma=3, closing_size=3)
Returns the labels for an image.
Segments using Canny edge-finding filter.
keyword arguments:
image -- The image in which to find particles
sigma -- The size of the Canny filter
closing_size -- The size of the closing filter
"""
class StretchedExponentialFTModel(Model):
r"""Fourier transform of the symmetrized stretched exponential
.. math::
S(E) = A \int_{-\infty}^{\infty} dt/h e^{-i2\pi(E-E_0)t/h} e^{|\frac{x}{\tau}|^\beta}
Normalization and maximum at :math:`E=E_0`:
.. math::
\int_{-\infty}^{\infty} dE S(E) = A
max(S) = A \frac{\tau}{\beta} \Gamma(\beta^{-1})
Uses scipy.fftpack.fft for the Fourier transform
Fitting parameters:
- integrated intensity ``amplitude`` :math:`A`
- position of the peak ``center`` :math:`E_0`
- nominal relaxation time ``tau``` :math:`\tau`
- stretching exponent ``beta`` :math:`\beta`
If the time unit is picoseconds, then the reciprocal energy unit is mili-eV
""" # noqa: E501
def __init__(self,
independent_vars=['x'],
prefix='',
missing=None,
name=None,
**kwargs):
kwargs.update({
'prefix': prefix,
'missing': missing,
'independent_vars': independent_vars
})
super(StretchedExponentialFTModel, self).__init__(strexpft, **kwargs)
self.set_param_hint('amplitude', min=0)
self.set_param_hint('tau', min=0)
self.set_param_hint('beta', min=0)
if version(lmfit.__version__) > version('0.9.5'):
__init__.__doc__ = lmfit.models.COMMON_INIT_DOC
def guess(self, y, x=None, **kwargs):
r"""Guess starting values for the parameters of a model.
Parameters
----------
y : :class:`~numpy:numpy.ndarray`
Intensities
x : :class:`~numpy:numpy.ndarray`
energy values
kwargs : dict
additional optional arguments, passed to model function.
Returns
-------
:class:`~lmfit.parameter.Parameters`
parameters with guessed values
"""
amplitude = 1.0
center = 0.0
tau = 10.0
beta = 1.0
if x is not None:
center = x[index_of(y, max(y))] # assumed peak within domain x
# Assumptions:
# 1. large dynamic range, function decays fast in domain x
# 2. x-values are equispaced
amplitude = sum(y) * (max(x) - min(x)) / len(x)
tau = max(y) / amplitude # assumed beta==1.0
return self.make_params(amplitude=amplitude,
center=center,
tau=tau,
beta=beta)
def __init__(self, fc=936.6e6, ppm=0, samp_rate_in=1625000.0 / 6.0 * 4.0):
gr.hier_block2.__init__(
self,
"Clock offset corrector",
gr.io_signature(1, 1, gr.sizeof_gr_complex * 1),
gr.io_signature(1, 1, gr.sizeof_gr_complex * 1),
)
if version(gr.version()) >= version('3.7.9'):
self.message_port_register_hier_in("ppm_in")
else:
self.message_port_register_hier_out("ppm_in")
##################################################
# Parameters
##################################################
self.fc = fc
self.ppm = ppm
self.samp_rate_in = samp_rate_in
##################################################
# Variables
##################################################
self.samp_rate_out = samp_rate_out = samp_rate_in
##################################################
# Blocks
##################################################
self.gsm_controlled_rotator_cc_0 = grgsm.controlled_rotator_cc(
0, samp_rate_out)
self.gsm_controlled_const_source_f_0 = grgsm.controlled_const_source_f(
ppm)
self.fractional_resampler_xx_0 = filter.fractional_resampler_cc(
0, samp_rate_in / samp_rate_out)
self.blocks_multiply_const_vxx_0_0 = blocks.multiply_const_vff(
(1.0e-6 * samp_rate_in / samp_rate_out, ))
self.blocks_multiply_const_vxx_0 = blocks.multiply_const_vff(
(fc / samp_rate_out * (2 * math.pi) / 1e6, ))
self.blocks_add_const_vxx_0 = blocks.add_const_vff(
(samp_rate_in / samp_rate_out, ))
##################################################
# Connections
##################################################
self.connect((self, 0), (self.fractional_resampler_xx_0, 0))
self.connect((self.fractional_resampler_xx_0, 0),
(self.gsm_controlled_rotator_cc_0, 0))
self.connect((self.blocks_add_const_vxx_0, 0),
(self.fractional_resampler_xx_0, 1))
self.connect((self.blocks_multiply_const_vxx_0_0, 0),
(self.blocks_add_const_vxx_0, 0))
self.connect((self.blocks_multiply_const_vxx_0, 0),
(self.gsm_controlled_rotator_cc_0, 1))
self.connect((self.gsm_controlled_rotator_cc_0, 0), (self, 0))
self.connect((self.gsm_controlled_const_source_f_0, 0),
(self.blocks_multiply_const_vxx_0_0, 0))
self.connect((self.gsm_controlled_const_source_f_0, 0),
(self.blocks_multiply_const_vxx_0, 0))
##################################################
# Asynch Message Connections
##################################################
self.msg_connect(self, "ppm_in", self.gsm_controlled_const_source_f_0,
"constant_msg")
class TeixeiraWaterModel(Model):
r"""This fitting function models the dynamic structure factor
for a particle undergoing jump diffusion.
J. Teixeira, M.-C. Bellissent-Funel, S. H. Chen, and A. J. Dianoux. `Phys. Rev. A, 31:1913-1917 <http://dx.doi.org/10.1103/PhysRevA.31.1913>`__
.. math::
S(Q,E) = \frac{A}{\pi} \cdot \frac{\Gamma}{\Gamma^2+(E-E_0)^2}
.. math::
\Gamma = \frac{\hbar\cdot D\cdot Q^2}{1+D\cdot Q^2\cdot \tau}
:math:`\Gamma` is the HWHM of the lorentzian curve.
At 298K and 1atm, water has :math:`D=2.30 10^{-5} cm^2/s` and
:math:`\tau=1.25 ps`.
A jump length :math:`l` can be associated: :math:`l^2=2N\cdot D\cdot \tau`,
where :math:`N` is the dimensionality of the diffusion problem
(:math:`N=3` for diffusion in a volume).
Fitting parameters:
- integrated intensity ``amplitude`` :math:`A`
- position of the peak ``center`` :math:`E_0`
- residence time ``center`` :math:`\tau`
- diffusion coefficient ``dcf`` :math:`D`
Attributes:
- Momentum transfer ``q``
""" # noqa: E501
def __init__(self,
independent_vars=['x'],
q=0.0,
prefix='',
missing=None,
name=None,
**kwargs):
kwargs.update({
'prefix': prefix,
'missing': missing,
'name': name,
'independent_vars': independent_vars
})
self.q = q
def txr(x, amplitude=1.0, center=1.0, tau=1.0, dcf=1.0):
r"""Teixeira intensities with a particular Q-value
Not implemented as partial(teixeira_water, q=q) because
inspect.getargspec faults with partial objects in python 2.7"""
return teixeira_water(x,
amplitude=amplitude,
center=center,
tau=tau,
dcf=dcf,
q=q)
super(TeixeiraWaterModel, self).__init__(txr, **kwargs)
[
self.set_param_hint(name, min=MIN_POS_DBL)
for name in ('amplitude', 'tau', 'dcf')
]
self.set_param_hint('fwhm', expr=self.fwhm_expr)
self.set_param_hint('height', expr=self.height_expr)
if version(lmfit.__version__) > version('0.9.5'):
__init__.__doc__ = lmfit.models.COMMON_INIT_DOC
@property
@prefix_params
def fwhm_expr(self):
"""Constraint expression for FWHM"""
dq2 = 'dcf*{q2}'.format(q2=self.q * self.q)
fmt = '2*{hbar}*{dq2}/(1+tau*{dq2})'
return fmt.format(hbar=hbar, dq2=dq2)
@property
@prefix_params
def height_expr(self):
"""Constraint expression for maximum peak height."""
fmt = "2.0/{pi}*amplitude/fwhm"
return fmt.format(pi=np.pi, prefix=self.prefix)
def guess(self, y, x=None, **kwargs):
r"""Guess starting values for the parameters of a model.
Parameters
----------
y : :class:`~numpy:numpy.ndarray`
Intensities
x : :class:`~numpy:numpy.ndarray`
energy values
kwargs : dict
additional optional arguments, passed to model function.
Returns
-------
:class:`~lmfit.parameter.Parameters`
parameters with guessed values
"""
amplitude = 1.0
center = 0.0
tau = 1.0
dcf = 1.0
if x is not None:
# Use guess method from the Lorentzian model
p = LorentzianModel().guess(y, x)
center = p['center']
# Assume diff*q*q and tau^(-1) same value
tau = hbar / (2 * p['sigma'])
dcf = 1.0 / (self.q * self.q * tau)
return self.make_params(amplitude=amplitude,
center=center,
tau=tau,
dcf=dcf)
"""
Created on Thu Jan 14 11:51:09 2016
@author: ibackus
"""
import scipy
from scipy.interpolate import InterpolatedUnivariateSpline as spline
from warnings import warn
import numpy as np
from distutils.version import LooseVersion as version
# InterpolatedUnivariateSpline in older versions of scipy don't handle regions
# outside the bbox and don't have the argument ext=0
if version(scipy.__version__) < '0.16.0':
warn('WARNING: Deprecated version of scipy. Please upgrade to at least 0.16.0')
spl = spline
# OVERRIDE spline if scipy is outdated
def spline(x, y, w=None, bbox=[None]*2, k=3, ext=0, check_finite=False):
splobj = spl(x, y, w, bbox, k)
bbox = list(splobj._data[3:5])
if ext == 'zeros':
ext = 0
def splfcn(xpts):
#! /usr/bin/env python3
import sys
import subprocess
from distutils.version import LooseVersion as version
assert len(sys.argv) == 3
inreq_path, outreq_path = sys.argv[1:]
def libv(s):
s = str(s).strip()
return s.split('==') if '==' in s else s.split('>=')
txt = subprocess.check_output(['pip3', 'list', '--format=freeze'])
txt = txt.decode('ascii', 'ignore')
installed = {}
for line in txt.split():
lib, v = libv(line)
installed[lib] = version(v)
with open(inreq_path) as fin, \
open(outreq_path, 'w') as fout:
for line in fin:
rlib, rv = libv(line)
if (rlib not in installed or version(rv) > installed[rlib]):
fout.write(line)
"""
Created on Thu Jan 14 11:51:09 2016
@author: ibackus
"""
import scipy
from scipy.interpolate import InterpolatedUnivariateSpline as spline
from warnings import warn
import numpy as np
from distutils.version import LooseVersion as version
# InterpolatedUnivariateSpline in older versions of scipy don't handle regions
# outside the bbox and don't have the argument ext=0
if version(scipy.__version__) < '0.16.0':
warn(
'WARNING: Deprecated version of scipy. Please upgrade to at least 0.16.0'
)
spl = spline
# OVERRIDE spline if scipy is outdated
def spline(x, y, w=None, bbox=[None] * 2, k=3, ext=0, check_finite=False):
splobj = spl(x, y, w, bbox, k)
bbox = list(splobj._data[3:5])
if ext == 'zeros':
ext = 0
