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ZELLMECHANIK-DRESDEN/dclab | dclab/features/fl_crosstalk.py | get_compensation_matrix | def get_compensation_matrix(ct21, ct31, ct12, ct32, ct13, ct23):
"""Compute crosstalk inversion matrix
The spillover matrix is
| | c11 c12 c13 |
| | c21 c22 c23 |
| | c31 c32 c33 |
The diagonal elements are set to 1, i.e.
ct11 = c22 = c33 = 1
Parameters
----------
cij: float... | python | def get_compensation_matrix(ct21, ct31, ct12, ct32, ct13, ct23):
"""Compute crosstalk inversion matrix
The spillover matrix is
| | c11 c12 c13 |
| | c21 c22 c23 |
| | c31 c32 c33 |
The diagonal elements are set to 1, i.e.
ct11 = c22 = c33 = 1
Parameters
----------
cij: float... | [
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ZELLMECHANIK-DRESDEN/dclab | dclab/features/fl_crosstalk.py | correct_crosstalk | def correct_crosstalk(fl1, fl2, fl3, fl_channel,
ct21=0, ct31=0, ct12=0, ct32=0, ct13=0, ct23=0):
"""Perform crosstalk correction
Parameters
----------
fli: int, float, or np.ndarray
Measured fluorescence signals
fl_channel: int (1, 2, or 3)
The channel number ... | python | def correct_crosstalk(fl1, fl2, fl3, fl_channel,
ct21=0, ct31=0, ct12=0, ct32=0, ct13=0, ct23=0):
"""Perform crosstalk correction
Parameters
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fli: int, float, or np.ndarray
Measured fluorescence signals
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The channel number ... | [
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ZELLMECHANIK-DRESDEN/dclab | dclab/features/inert_ratio.py | cont_moments_cv | def cont_moments_cv(cont,
flt_epsilon=1.19209e-07,
dbl_epsilon=2.2204460492503131e-16):
"""Compute the moments of a contour
The moments are computed in the same way as they are computed
in OpenCV's `contourMoments` in `moments.cpp`.
Parameters
----------
... | python | def cont_moments_cv(cont,
flt_epsilon=1.19209e-07,
dbl_epsilon=2.2204460492503131e-16):
"""Compute the moments of a contour
The moments are computed in the same way as they are computed
in OpenCV's `contourMoments` in `moments.cpp`.
Parameters
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ZELLMECHANIK-DRESDEN/dclab | dclab/features/inert_ratio.py | get_inert_ratio_cvx | def get_inert_ratio_cvx(cont):
"""Compute the inertia ratio of the convex hull of a contour
The inertia ratio is computed from the central second order of moments
along x (mu20) and y (mu02) via `sqrt(mu20/mu02)`.
Parameters
----------
cont: ndarray or list of ndarrays of shape (N,2)
A... | python | def get_inert_ratio_cvx(cont):
"""Compute the inertia ratio of the convex hull of a contour
The inertia ratio is computed from the central second order of moments
along x (mu20) and y (mu02) via `sqrt(mu20/mu02)`.
Parameters
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cont: ndarray or list of ndarrays of shape (N,2)
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ZELLMECHANIK-DRESDEN/dclab | dclab/features/inert_ratio.py | get_inert_ratio_prnc | def get_inert_ratio_prnc(cont):
"""Compute principal inertia ratio of a contour
The principal inertia ratio is rotation-invariant, which
makes it applicable to reservoir measurements where e.g.
cells are not aligned with the channel.
Parameters
----------
cont: ndarray or list of ndarrays ... | python | def get_inert_ratio_prnc(cont):
"""Compute principal inertia ratio of a contour
The principal inertia ratio is rotation-invariant, which
makes it applicable to reservoir measurements where e.g.
cells are not aligned with the channel.
Parameters
----------
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ZELLMECHANIK-DRESDEN/dclab | dclab/features/inert_ratio.py | get_inert_ratio_raw | def get_inert_ratio_raw(cont):
"""Compute the inertia ratio of a contour
The inertia ratio is computed from the central second order of moments
along x (mu20) and y (mu02) via `sqrt(mu20/mu02)`.
Parameters
----------
cont: ndarray or list of ndarrays of shape (N,2)
A 2D array that hold... | python | def get_inert_ratio_raw(cont):
"""Compute the inertia ratio of a contour
The inertia ratio is computed from the central second order of moments
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Parameters
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cont: ndarray or list of ndarrays of shape (N,2)
A 2D array that hold... | [
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ZELLMECHANIK-DRESDEN/dclab | dclab/features/inert_ratio.py | get_tilt | def get_tilt(cont):
"""Compute tilt of raw contour relative to channel axis
Parameters
----------
cont: ndarray or list of ndarrays of shape (N,2)
A 2D array that holds the contour of an event (in pixels)
e.g. obtained using `mm.contour` where `mm` is an instance
of `RTDCBase`.... | python | def get_tilt(cont):
"""Compute tilt of raw contour relative to channel axis
Parameters
----------
cont: ndarray or list of ndarrays of shape (N,2)
A 2D array that holds the contour of an event (in pixels)
e.g. obtained using `mm.contour` where `mm` is an instance
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deep-compute/funcserver | funcserver/funcserver.py | tag | def tag(*tags):
'''
Constructs a decorator that tags a function with specified
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'''
def dfn(fn):
_tags = getattr(fn, 'tags', set())
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fn.tags = _tags
return fn
return... | python | def tag(*tags):
'''
Constructs a decorator that tags a function with specified
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'''
def dfn(fn):
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deep-compute/funcserver | funcserver/funcserver.py | raw | def raw(mime='application/octet-stream'):
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deep-compute/funcserver | funcserver/funcserver.py | WSConnection.open | def open(self, pysession_id):
'''
Called when client opens connection. Initialization
is done here.
'''
self.id = id(self)
self.funcserver = self.application.funcserver
self.pysession_id = pysession_id
# register this connection with node
self.sta... | python | def open(self, pysession_id):
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Called when client opens connection. Initialization
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self.id = id(self)
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deep-compute/funcserver | funcserver/funcserver.py | WSConnection.on_message | def on_message(self, msg):
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Currently the only implementation of the python
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'''
Called when client sends a message.
Supports a python debugging console. This forms
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deep-compute/funcserver | funcserver/funcserver.py | WSConnection.on_close | def on_close(self):
'''
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deep-compute/funcserver | funcserver/funcserver.py | RPCHandler._clean_kwargs | def _clean_kwargs(self, kwargs, fn):
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deep-compute/funcserver | funcserver/funcserver.py | Server.dump_stacks | def dump_stacks(self):
'''
Dumps the stack of all threads. This function
is meant for debugging. Useful when a deadlock happens.
borrowed from: http://blog.ziade.org/2012/05/25/zmq-and-gevent-debugging-nightmares/
'''
dump = []
# threads
threads = dict(... | python | def dump_stacks(self):
'''
Dumps the stack of all threads. This function
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deep-compute/funcserver | funcserver/funcserver.py | Server.define_log_pre_format_hooks | def define_log_pre_format_hooks(self):
"""
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"""
hooks = super(Server, self).define_log_pre_format_hooks()
# NOTE enabling logs only on debug mode
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... | python | def define_log_pre_format_hooks(self):
"""
adds a hook to send to websocket if the run command was selected
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openstax/cnx-archive | cnxarchive/scripts/export_epub/db.py | _get_sql | def _get_sql(filename):
"""Returns the contents of the sql file from the given ``filename``."""
with open(os.path.join(SQL_DIR, filename), 'r') as f:
return f.read() | python | def _get_sql(filename):
"""Returns the contents of the sql file from the given ``filename``."""
with open(os.path.join(SQL_DIR, filename), 'r') as f:
return f.read() | [
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openstax/cnx-archive | cnxarchive/scripts/export_epub/db.py | verify_id_n_version | def verify_id_n_version(id, version):
"""Given an ``id`` and ``version``, verify the identified content exists.
"""
stmt = _get_sql('verify-id-and-version.sql')
args = dict(id=id, version=version)
with db_connect() as db_conn:
with db_conn.cursor() as cursor:
cursor.execute(stm... | python | def verify_id_n_version(id, version):
"""Given an ``id`` and ``version``, verify the identified content exists.
"""
stmt = _get_sql('verify-id-and-version.sql')
args = dict(id=id, version=version)
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with db_conn.cursor() as cursor:
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openstax/cnx-archive | cnxarchive/scripts/export_epub/db.py | get_id_n_version | def get_id_n_version(ident_hash):
"""From the given ``ident_hash`` return the id and version."""
try:
id, version = split_ident_hash(ident_hash)
except IdentHashMissingVersion:
# XXX Don't import from views... And don't use httpexceptions
from pyramid.httpexceptions import HTTPNotFou... | python | def get_id_n_version(ident_hash):
"""From the given ``ident_hash`` return the id and version."""
try:
id, version = split_ident_hash(ident_hash)
except IdentHashMissingVersion:
# XXX Don't import from views... And don't use httpexceptions
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openstax/cnx-archive | cnxarchive/scripts/export_epub/db.py | get_type | def get_type(ident_hash):
"""Return the database type for the given ``ident_hash``
As of now, this could either be a 'Module' or 'Collection'.
"""
id, version = get_id_n_version(ident_hash)
stmt = _get_sql('get-type.sql')
args = dict(id=id, version=version)
with db_connect() as db_conn:
... | python | def get_type(ident_hash):
"""Return the database type for the given ``ident_hash``
As of now, this could either be a 'Module' or 'Collection'.
"""
id, version = get_id_n_version(ident_hash)
stmt = _get_sql('get-type.sql')
args = dict(id=id, version=version)
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openstax/cnx-archive | cnxarchive/scripts/export_epub/db.py | get_metadata | def get_metadata(ident_hash):
"""Return the dictionary of metadata from the database.
This data is keyed using the cnx-epub data structure.
"""
id, version = get_id_n_version(ident_hash)
stmt = _get_sql('get-metadata.sql')
args = dict(id=id, version=version)
# FIXME The license_url and li... | python | def get_metadata(ident_hash):
"""Return the dictionary of metadata from the database.
This data is keyed using the cnx-epub data structure.
"""
id, version = get_id_n_version(ident_hash)
stmt = _get_sql('get-metadata.sql')
args = dict(id=id, version=version)
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openstax/cnx-archive | cnxarchive/scripts/export_epub/db.py | get_content | def get_content(ident_hash, context=None):
"""Returns the content for the given ``ident_hash``.
``context`` is optionally ident-hash used to find the content
within the context of a Collection ident_hash.
"""
id, version = get_id_n_version(ident_hash)
filename = 'index.cnxml.html'
if conte... | python | def get_content(ident_hash, context=None):
"""Returns the content for the given ``ident_hash``.
``context`` is optionally ident-hash used to find the content
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"""
id, version = get_id_n_version(ident_hash)
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openstax/cnx-archive | cnxarchive/scripts/export_epub/db.py | get_file_info | def get_file_info(hash, context=None):
"""Returns information about the file, identified by ``hash``.
If the `context` (an ident-hash) is supplied,
the information returned will be specific to that context.
"""
if context is None:
stmt = _get_sql('get-file-info.sql')
args = dict(has... | python | def get_file_info(hash, context=None):
"""Returns information about the file, identified by ``hash``.
If the `context` (an ident-hash) is supplied,
the information returned will be specific to that context.
"""
if context is None:
stmt = _get_sql('get-file-info.sql')
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openstax/cnx-archive | cnxarchive/scripts/export_epub/db.py | get_file | def get_file(hash):
"""Return the contents of the file as a ``memoryview``."""
stmt = _get_sql('get-file.sql')
args = dict(hash=hash)
with db_connect() as db_conn:
with db_conn.cursor() as cursor:
cursor.execute(stmt, args)
try:
file, _ = cursor.fetchone(... | python | def get_file(hash):
"""Return the contents of the file as a ``memoryview``."""
stmt = _get_sql('get-file.sql')
args = dict(hash=hash)
with db_connect() as db_conn:
with db_conn.cursor() as cursor:
cursor.execute(stmt, args)
try:
file, _ = cursor.fetchone(... | [
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openstax/cnx-archive | cnxarchive/scripts/export_epub/db.py | get_registered_files | def get_registered_files(ident_hash):
"""Returns a list SHA1 hashes for registered file entries
identified by the given module ``ident_hash``.
Note, it's possible for a module to reference a file without having
a registered file entry for it.
Note, all files are included, including the raw form of... | python | def get_registered_files(ident_hash):
"""Returns a list SHA1 hashes for registered file entries
identified by the given module ``ident_hash``.
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openstax/cnx-archive | cnxarchive/scripts/export_epub/db.py | get_tree | def get_tree(ident_hash, baked=False):
"""Return a tree structure of the Collection"""
id, version = get_id_n_version(ident_hash)
stmt = _get_sql('get-tree.sql')
args = dict(id=id, version=version, baked=baked)
with db_connect() as db_conn:
with db_conn.cursor() as cursor:
curs... | python | def get_tree(ident_hash, baked=False):
"""Return a tree structure of the Collection"""
id, version = get_id_n_version(ident_hash)
stmt = _get_sql('get-tree.sql')
args = dict(id=id, version=version, baked=baked)
with db_connect() as db_conn:
with db_conn.cursor() as cursor:
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openstax/cnx-archive | cnxarchive/scripts/inject_resource.py | guess_media_type | def guess_media_type(filepath):
"""Returns the media-type of the file at the given ``filepath``"""
o = subprocess.check_output(['file', '--mime-type', '-Lb', filepath])
o = o.strip()
return o | python | def guess_media_type(filepath):
"""Returns the media-type of the file at the given ``filepath``"""
o = subprocess.check_output(['file', '--mime-type', '-Lb', filepath])
o = o.strip()
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openstax/cnx-archive | cnxarchive/scripts/inject_resource.py | lookup_module_ident | def lookup_module_ident(id, version):
"""Return the ``module_ident`` for the given ``id`` &
major and minor version as a tuple.
"""
with db_connect() as db_conn:
with db_conn.cursor() as cursor:
cursor.execute(
"SELECT module_ident FROM modules "
"WHE... | python | def lookup_module_ident(id, version):
"""Return the ``module_ident`` for the given ``id`` &
major and minor version as a tuple.
"""
with db_connect() as db_conn:
with db_conn.cursor() as cursor:
cursor.execute(
"SELECT module_ident FROM modules "
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openstax/cnx-archive | cnxarchive/scripts/inject_resource.py | insert_file | def insert_file(file, media_type):
"""Upsert the ``file`` and ``media_type`` into the files table.
Returns the ``fileid`` and ``sha1`` of the upserted file.
"""
resource_hash = get_file_sha1(file)
with db_connect() as db_conn:
with db_conn.cursor() as cursor:
cursor.execute("SEL... | python | def insert_file(file, media_type):
"""Upsert the ``file`` and ``media_type`` into the files table.
Returns the ``fileid`` and ``sha1`` of the upserted file.
"""
resource_hash = get_file_sha1(file)
with db_connect() as db_conn:
with db_conn.cursor() as cursor:
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openstax/cnx-archive | cnxarchive/scripts/inject_resource.py | upsert_module_file | def upsert_module_file(module_ident, fileid, filename):
"""Upsert a file associated with ``fileid`` with ``filename``
as a module_files entry associated with content at ``module_ident``.
"""
with db_connect() as db_conn:
with db_conn.cursor() as cursor:
cursor.execute("SELECT true F... | python | def upsert_module_file(module_ident, fileid, filename):
"""Upsert a file associated with ``fileid`` with ``filename``
as a module_files entry associated with content at ``module_ident``.
"""
with db_connect() as db_conn:
with db_conn.cursor() as cursor:
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openstax/cnx-archive | cnxarchive/scripts/inject_resource.py | inject_resource | def inject_resource(ident_hash, file, filename, media_type):
"""Injects the contents of ``file`` (a file-like object) into the database
as ``filename`` with ``media_type`` in association with the content
at ``ident_hash``.
"""
resource_hash = get_file_sha1(file)
with db_connect() as db_conn:
... | python | def inject_resource(ident_hash, file, filename, media_type):
"""Injects the contents of ``file`` (a file-like object) into the database
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ZELLMECHANIK-DRESDEN/dclab | dclab/features/contour.py | get_contour | def get_contour(mask):
"""Compute the image contour from a mask
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Parameters
----------
mask: binary ndarray of shape (M,N) or (K,M,N)
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"""Compute the image contour from a mask
The contour is computed in a very inefficient way using scikit-image
and a conversion of float coordinates to pixel coordinates.
Parameters
----------
mask: binary ndarray of shape (M,N) or (K,M,N)
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simse/pymitv | pymitv/discover.py | Discover.scan | def scan(self, stop_on_first=True, base_ip=0):
"""Scans the local network for TVs."""
tvs = []
# Check if base_ip has been passed
if base_ip == 0:
# Find IP address of computer pymitv is running on
sock = socket.socket(socket.AF_INET, socket.SOCK_DGRAM)
... | python | def scan(self, stop_on_first=True, base_ip=0):
"""Scans the local network for TVs."""
tvs = []
# Check if base_ip has been passed
if base_ip == 0:
# Find IP address of computer pymitv is running on
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simse/pymitv | pymitv/discover.py | Discover.check_ip | def check_ip(ip, log=False):
"""Attempts a connection to the TV and checks if there really is a TV."""
if log:
print('Checking ip: {}...'.format(ip))
request_timeout = 0.1
try:
tv_url = 'http://{}:6095/request?action=isalive'.format(ip)
requ... | python | def check_ip(ip, log=False):
"""Attempts a connection to the TV and checks if there really is a TV."""
if log:
print('Checking ip: {}...'.format(ip))
request_timeout = 0.1
try:
tv_url = 'http://{}:6095/request?action=isalive'.format(ip)
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xenon-middleware/pyxenon | xenon/oop.py | get_field_type | def get_field_type(f):
"""Obtain the type name of a GRPC Message field."""
types = (t[5:] for t in dir(f) if t[:4] == 'TYPE' and
getattr(f, t) == f.type)
return next(types) | python | def get_field_type(f):
"""Obtain the type name of a GRPC Message field."""
types = (t[5:] for t in dir(f) if t[:4] == 'TYPE' and
getattr(f, t) == f.type)
return next(types) | [
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xenon-middleware/pyxenon | xenon/oop.py | get_field_description | def get_field_description(f):
"""Get the type description of a GRPC Message field."""
type_name = get_field_type(f)
if type_name == 'MESSAGE' and \
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return 'map<string, string>'
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return ... | python | def get_field_description(f):
"""Get the type description of a GRPC Message field."""
type_name = get_field_type(f)
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xenon-middleware/pyxenon | xenon/oop.py | make_static_request | def make_static_request(method, *args, **kwargs):
"""Creates a request from a static method function call."""
if args and not use_signature:
raise NotImplementedError("Only keyword arguments allowed in Python2")
if use_signature:
new_kwargs = {kw: unwrap(value) for kw, value in kwargs.items... | python | def make_static_request(method, *args, **kwargs):
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xenon-middleware/pyxenon | xenon/oop.py | make_request | def make_request(self, method, *args, **kwargs):
"""Creates a request from a method function call."""
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new_kwargs = {kw: unwrap(value) for kw, value in kwargs.items()}
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xenon-middleware/pyxenon | xenon/oop.py | method_wrapper | def method_wrapper(m):
"""Generates a method from a `GrpcMethod` definition."""
if m.is_simple:
def simple_method(self):
"""TODO: no docstring!"""
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"""Generates a method from a `GrpcMethod` definition."""
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xenon-middleware/pyxenon | xenon/oop.py | GrpcMethod.request_name | def request_name(self):
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return 'Empty'
if not self.uses_request:
return None
if isinstance(self.uses_request, str):
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"""Generate the name of the request."""
if self.static and not self.uses_request:
return 'Empty'
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return None
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xenon-middleware/pyxenon | xenon/oop.py | GrpcMethod.request_type | def request_type(self):
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if self.static and not self.uses_request:
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xenon-middleware/pyxenon | xenon/oop.py | GrpcMethod.signature | def signature(self):
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parameters = \
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"""Create a signature for this method, only in Python > 3.4"""
if not use_signature:
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xenon-middleware/pyxenon | xenon/oop.py | GrpcMethod.docstring | def docstring(self, servicer):
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if self.uses_request:
s += "\n"
for field in get_fields(self.request_type):
if f... | python | def docstring(self, servicer):
"""Generate a doc-string."""
s = getattr(servicer, to_lower_camel_case(self.name)).__doc__ \
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openstax/cnx-archive | cnxarchive/utils/text.py | slugify | def slugify(string):
"""Return a slug for the unicode_string.
(lowercase, only letters and numbers, hyphens replace spaces)
"""
filtered_string = []
if isinstance(string, str):
string = unicode(string, 'utf-8')
for i in unicodedata.normalize('NFKC', string):
cat = unicodedata.ca... | python | def slugify(string):
"""Return a slug for the unicode_string.
(lowercase, only letters and numbers, hyphens replace spaces)
"""
filtered_string = []
if isinstance(string, str):
string = unicode(string, 'utf-8')
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openstax/cnx-archive | cnxarchive/utils/text.py | utf8 | def utf8(item):
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if isinstance(item, tuple):
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return {utf8(k): utf8(v) for k, v in item.it... | python | def utf8(item):
"""Change all python2 str/bytes instances to unicode/python3 str."""
if isinstance(item, list):
return [utf8(i) for i in item]
if isinstance(item, tuple):
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ZELLMECHANIK-DRESDEN/dclab | dclab/rtdc_dataset/filter.py | Filter.update | def update(self, force=[]):
"""Update the filters according to `self.rtdc_ds.config["filtering"]`
Parameters
----------
force : list
A list of feature names that must be refiltered with
min/max values.
"""
# These lists may help us become very fa... | python | def update(self, force=[]):
"""Update the filters according to `self.rtdc_ds.config["filtering"]`
Parameters
----------
force : list
A list of feature names that must be refiltered with
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ZELLMECHANIK-DRESDEN/dclab | dclab/external/skimage/_find_contours.py | find_contours | def find_contours(array, level,
fully_connected='low', positive_orientation='low'):
"""Find iso-valued contours in a 2D array for a given level value.
Uses the "marching squares" method to compute a the iso-valued contours of
the input 2D array for a particular level value. Array values a... | python | def find_contours(array, level,
fully_connected='low', positive_orientation='low'):
"""Find iso-valued contours in a 2D array for a given level value.
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openstax/cnx-archive | cnxarchive/database.py | get_module_ident_from_ident_hash | def get_module_ident_from_ident_hash(ident_hash, cursor):
"""Return the moduleid for a given ``ident_hash``."""
try:
uuid, (mj_ver, mn_ver) = split_ident_hash(
ident_hash, split_version=True)
except IdentHashMissingVersion as e:
uuid, mj_ver, mn_ver = e.id, None, None
args = ... | python | def get_module_ident_from_ident_hash(ident_hash, cursor):
"""Return the moduleid for a given ``ident_hash``."""
try:
uuid, (mj_ver, mn_ver) = split_ident_hash(
ident_hash, split_version=True)
except IdentHashMissingVersion as e:
uuid, mj_ver, mn_ver = e.id, None, None
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openstax/cnx-archive | cnxarchive/database.py | get_tree | def get_tree(ident_hash, cursor, as_collated=False):
"""Return a JSON representation of the binder tree for ``ident_hash``."""
uuid, version = split_ident_hash(ident_hash)
cursor.execute(SQL['get-tree-by-uuid-n-version'],
(uuid, version, as_collated,))
try:
tree = cursor.fetch... | python | def get_tree(ident_hash, cursor, as_collated=False):
"""Return a JSON representation of the binder tree for ``ident_hash``."""
uuid, version = split_ident_hash(ident_hash)
cursor.execute(SQL['get-tree-by-uuid-n-version'],
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openstax/cnx-archive | cnxarchive/database.py | get_collated_content | def get_collated_content(ident_hash, context_ident_hash, cursor):
"""Return collated content for ``ident_hash``."""
cursor.execute(SQL['get-collated-content'],
(ident_hash, context_ident_hash,))
try:
return cursor.fetchone()[0]
except TypeError: # NoneType
return | python | def get_collated_content(ident_hash, context_ident_hash, cursor):
"""Return collated content for ``ident_hash``."""
cursor.execute(SQL['get-collated-content'],
(ident_hash, context_ident_hash,))
try:
return cursor.fetchone()[0]
except TypeError: # NoneType
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openstax/cnx-archive | cnxarchive/database.py | get_module_uuid | def get_module_uuid(plpy, moduleid):
"""Retrieve page uuid from legacy moduleid."""
plan = plpy.prepare("SELECT uuid FROM modules WHERE moduleid = $1;",
('text',))
result = plpy.execute(plan, (moduleid,), 1)
if result:
return result[0]['uuid'] | python | def get_module_uuid(plpy, moduleid):
"""Retrieve page uuid from legacy moduleid."""
plan = plpy.prepare("SELECT uuid FROM modules WHERE moduleid = $1;",
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result = plpy.execute(plan, (moduleid,), 1)
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openstax/cnx-archive | cnxarchive/database.py | get_current_module_ident | def get_current_module_ident(moduleid, plpy):
"""Retrieve module_ident for a given moduleid.
Note that module_ident is used only for internal database relational
associations, and is equivalent to a uuid@version for a given document.
"""
plan = plpy.prepare('''\
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"""Retrieve module_ident for a given moduleid.
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openstax/cnx-archive | cnxarchive/database.py | get_minor_version | def get_minor_version(module_ident, plpy):
"""Retrieve minor version only given module_ident."""
# Make sure to always return the max minor version that is already in the
# database, in case the given module_ident is not the latest version
plan = plpy.prepare('''\
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SELECT ... | python | def get_minor_version(module_ident, plpy):
"""Retrieve minor version only given module_ident."""
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openstax/cnx-archive | cnxarchive/database.py | get_collections | def get_collections(module_ident, plpy):
"""Get all the collections that the module is part of."""
# Make sure to only return one match per collection and only if it is the
# latest collection (which may not be the same as what is in
# latest_modules)
plan = plpy.prepare('''
WITH RECURSIVE t(node, p... | python | def get_collections(module_ident, plpy):
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openstax/cnx-archive | cnxarchive/database.py | get_subcols | def get_subcols(module_ident, plpy):
"""Get all the sub-collections that the module is part of."""
plan = plpy.prepare('''
WITH RECURSIVE t(node, parent, path, document) AS (
SELECT tr.nodeid, tr.parent_id, ARRAY[tr.nodeid], tr.documentid
FROM trees tr
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openstax/cnx-archive | cnxarchive/database.py | rebuild_collection_tree | def rebuild_collection_tree(old_collection_ident, new_document_id_map, plpy):
"""Create a new tree for the collection based on the old tree.
This uses new document ids, replacing old ones.
"""
get_tree = plpy.prepare('''
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"""Create a new tree for the collection based on the old tree.
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openstax/cnx-archive | cnxarchive/database.py | republish_collection | def republish_collection(submitter, submitlog, next_minor_version,
collection_ident, plpy, revised=None):
"""Insert a new row for collection_ident with a new version.
Returns the module_ident of the row inserted.
"""
sql = '''
INSERT INTO modules (portal_type, moduleid, uui... | python | def republish_collection(submitter, submitlog, next_minor_version,
collection_ident, plpy, revised=None):
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openstax/cnx-archive | cnxarchive/database.py | set_version | def set_version(portal_type, legacy_version, td):
"""Set the major_version and minor_version if they are not set."""
modified = 'OK'
legacy_major, legacy_minor = legacy_version.split('.')
if portal_type == 'Collection':
# For collections, both major and minor needs to be set
modified = ... | python | def set_version(portal_type, legacy_version, td):
"""Set the major_version and minor_version if they are not set."""
modified = 'OK'
legacy_major, legacy_minor = legacy_version.split('.')
if portal_type == 'Collection':
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openstax/cnx-archive | cnxarchive/database.py | republish_module | def republish_module(td, plpy):
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openstax/cnx-archive | cnxarchive/database.py | republish_module_trigger | def republish_module_trigger(plpy, td):
"""Trigger called from postgres database when republishing a module.
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... | python | def republish_module_trigger(plpy, td):
"""Trigger called from postgres database when republishing a module.
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openstax/cnx-archive | cnxarchive/database.py | assign_moduleid_default_trigger | def assign_moduleid_default_trigger(plpy, td):
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cnx-publishing publications. This does NOT include
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openstax/cnx-archive | cnxarchive/database.py | assign_version_default_trigger | def assign_version_default_trigger(plpy, td):
"""Trigger to fill in legacy data fields.
A compatibilty trigger to fill in legacy data fields that are not
populated when inserting publications from cnx-publishing.
If this is not a legacy publication the ``version`` will be set
based on the ``major_... | python | def assign_version_default_trigger(plpy, td):
"""Trigger to fill in legacy data fields.
A compatibilty trigger to fill in legacy data fields that are not
populated when inserting publications from cnx-publishing.
If this is not a legacy publication the ``version`` will be set
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openstax/cnx-archive | cnxarchive/database.py | assign_document_controls_default_trigger | def assign_document_controls_default_trigger(plpy, td):
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A compatibilty trigger to fill in ``uuid`` and ``licenseid`` columns
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openstax/cnx-archive | cnxarchive/database.py | upsert_document_acl_trigger | def upsert_document_acl_trigger(plpy, td):
"""Trigger for filling in acls when legacy publishes.
A compatibility trigger to upsert authorization control entries (ACEs)
for legacy publications.
"""
modified_state = "OK"
uuid_ = td['new']['uuid']
authors = td['new']['authors'] and td['new']['... | python | def upsert_document_acl_trigger(plpy, td):
"""Trigger for filling in acls when legacy publishes.
A compatibility trigger to upsert authorization control entries (ACEs)
for legacy publications.
"""
modified_state = "OK"
uuid_ = td['new']['uuid']
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openstax/cnx-archive | cnxarchive/database.py | upsert_users_from_legacy_publication_trigger | def upsert_users_from_legacy_publication_trigger(plpy, td):
"""A compatibility trigger to upsert users from legacy persons table."""
modified_state = "OK"
authors = td['new']['authors'] and td['new']['authors'] or []
maintainers = td['new']['maintainers'] and td['new']['maintainers'] or []
licensors... | python | def upsert_users_from_legacy_publication_trigger(plpy, td):
"""A compatibility trigger to upsert users from legacy persons table."""
modified_state = "OK"
authors = td['new']['authors'] and td['new']['authors'] or []
maintainers = td['new']['maintainers'] and td['new']['maintainers'] or []
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openstax/cnx-archive | cnxarchive/database.py | insert_users_for_optional_roles_trigger | def insert_users_for_optional_roles_trigger(plpy, td):
"""Trigger to update users from optional roles entries.
A compatibility trigger to insert users from moduleoptionalroles
records. This is primarily for legacy compatibility, but it is not
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openstax/cnx-archive | cnxarchive/database.py | add_module_file | def add_module_file(plpy, td):
"""Database trigger for adding a module file.
When a legacy ``index.cnxml`` is added, this trigger
transforms it into html and stores it as ``index.cnxml.html``.
When a cnx-publishing ``index.cnxml.html`` is added, this trigger
checks if ``index.html.cnxml`` exists be... | python | def add_module_file(plpy, td):
"""Database trigger for adding a module file.
When a legacy ``index.cnxml`` is added, this trigger
transforms it into html and stores it as ``index.cnxml.html``.
When a cnx-publishing ``index.cnxml.html`` is added, this trigger
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openstax/cnx-archive | cnxarchive/database.py | _transform_abstract | def _transform_abstract(plpy, module_ident):
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Transforms an abstract using one of content columns
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will go (cnxml->html or html->cnxml).
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the... | python | def _transform_abstract(plpy, module_ident):
"""Transform abstract, bi-directionally.
Transforms an abstract using one of content columns
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will go (cnxml->html or html->cnxml).
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openstax/cnx-archive | cnxarchive/database.py | get_collection_tree | def get_collection_tree(collection_ident, cursor):
"""Build and retrieve json tree representation of a book."""
cursor.execute('''
WITH RECURSIVE t(node, parent, document, path) AS (
SELECT tr.nodeid, tr.parent_id, tr.documentid, ARRAY[tr.nodeid]
FROM trees tr
WHERE tr.documentid = %... | python | def get_collection_tree(collection_ident, cursor):
"""Build and retrieve json tree representation of a book."""
cursor.execute('''
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openstax/cnx-archive | cnxarchive/database.py | get_module_can_publish | def get_module_can_publish(cursor, id):
"""Return userids allowed to publish this book."""
cursor.execute("""
SELECT DISTINCT user_id
FROM document_acl
WHERE uuid = %s AND permission = 'publish'""", (id,))
return [i[0] for i in cursor.fetchall()] | python | def get_module_can_publish(cursor, id):
"""Return userids allowed to publish this book."""
cursor.execute("""
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FROM document_acl
WHERE uuid = %s AND permission = 'publish'""", (id,))
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openstax/cnx-archive | cnxarchive/scripts/export_epub/modeling.py | tree_to_nodes | def tree_to_nodes(tree, context=None, metadata=None):
"""Assembles ``tree`` nodes into object models.
If ``context`` is supplied, it will be used to contextualize
the contents of the nodes. Metadata will pass non-node identifying
values down to child nodes, if not overridden (license, timestamps, etc)
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openstax/cnx-archive | cnxarchive/scripts/export_epub/modeling.py | create_epub | def create_epub(ident_hash, file, format='raw'):
"""Creates an epub from an ``ident_hash``, which is output to the given
``file`` (a file-like object).
Returns None, writes to the given ``file``.
"""
model = factory(ident_hash, baked=(format != 'raw'))
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... | python | def create_epub(ident_hash, file, format='raw'):
"""Creates an epub from an ``ident_hash``, which is output to the given
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Returns None, writes to the given ``file``.
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openstax/cnx-archive | cnxarchive/views/exports.py | get_export | def get_export(request):
"""Retrieve an export file."""
settings = get_current_registry().settings
exports_dirs = settings['exports-directories'].split()
args = request.matchdict
ident_hash, type = args['ident_hash'], args['type']
id, version = split_ident_hash(ident_hash)
with db_connect()... | python | def get_export(request):
"""Retrieve an export file."""
settings = get_current_registry().settings
exports_dirs = settings['exports-directories'].split()
args = request.matchdict
ident_hash, type = args['ident_hash'], args['type']
id, version = split_ident_hash(ident_hash)
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openstax/cnx-archive | cnxarchive/views/exports.py | get_export_files | def get_export_files(cursor, id, version, types, exports_dirs, read_file=True):
"""Retrieve files associated with document."""
request = get_current_request()
type_info = dict(request.registry.settings['_type_info'])
metadata = get_content_metadata(id, version, cursor)
legacy_id = metadata['legacy_i... | python | def get_export_files(cursor, id, version, types, exports_dirs, read_file=True):
"""Retrieve files associated with document."""
request = get_current_request()
type_info = dict(request.registry.settings['_type_info'])
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openstax/cnx-archive | cnxarchive/views/helpers.py | get_content_metadata | def get_content_metadata(id, version, cursor):
"""Return metadata related to the content from the database."""
# Do the module lookup
args = dict(id=id, version=version)
# FIXME We are doing two queries here that can hopefully be
# condensed into one.
cursor.execute(SQL['get-module-metadat... | python | def get_content_metadata(id, version, cursor):
"""Return metadata related to the content from the database."""
# Do the module lookup
args = dict(id=id, version=version)
# FIXME We are doing two queries here that can hopefully be
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ZELLMECHANIK-DRESDEN/dclab | dclab/kde_contours.py | find_contours_level | def find_contours_level(density, x, y, level, closed=False):
"""Find iso-valued density contours for a given level value
Parameters
----------
density: 2d ndarray of shape (M, N)
Kernel density estimate for which to compute the contours
x: 2d ndarray of shape (M, N) or 1d ndarray of size M
... | python | def find_contours_level(density, x, y, level, closed=False):
"""Find iso-valued density contours for a given level value
Parameters
----------
density: 2d ndarray of shape (M, N)
Kernel density estimate for which to compute the contours
x: 2d ndarray of shape (M, N) or 1d ndarray of size M
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ZELLMECHANIK-DRESDEN/dclab | dclab/kde_contours.py | get_quantile_levels | def get_quantile_levels(density, x, y, xp, yp, q, normalize=True):
"""Compute density levels for given quantiles by interpolation
For a given 2D density, compute the density levels at which
the resulting contours contain the fraction `1-q` of all
data points. E.g. for a measurement of 1000 events, all
... | python | def get_quantile_levels(density, x, y, xp, yp, q, normalize=True):
"""Compute density levels for given quantiles by interpolation
For a given 2D density, compute the density levels at which
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ZELLMECHANIK-DRESDEN/dclab | dclab/kde_contours.py | _find_quantile_level | def _find_quantile_level(density, x, y, xp, yp, quantile, acc=.01,
ret_err=False):
"""Find density level for a given data quantile by iteration
Parameters
----------
density: 2d ndarray of shape (M, N)
Kernel density estimate for which to compute the contours
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density: 2d ndarray of shape (M, N)
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ZELLMECHANIK-DRESDEN/dclab | dclab/rtdc_dataset/write_hdf5.py | write | def write(path_or_h5file, data={}, meta={}, logs={}, mode="reset",
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"""Write data to an RT-DC file
Parameters
----------
path: path or h5py.File
The path or the hdf5 file object to write to.
data: dict-like
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path: path or h5py.File
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openstax/cnx-archive | cnxarchive/search.py | _convert | def _convert(tup, dictlist):
"""
:param tup: a list of tuples
:param di: a dictionary converted from tup
:return: dictionary
"""
di = {}
for a, b in tup:
di.setdefault(a, []).append(b)
for key, val in di.items():
dictlist.append((key, val))
return dictlist | python | def _convert(tup, dictlist):
"""
:param tup: a list of tuples
:param di: a dictionary converted from tup
:return: dictionary
"""
di = {}
for a, b in tup:
di.setdefault(a, []).append(b)
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"""
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"""
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res.append(ele.upper())
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"""
:param val_list: a list of strings
:return: a list of upper-cased strings
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openstax/cnx-archive | cnxarchive/search.py | _build_search | def _build_search(structured_query):
"""Construct search statment for db execution.
Produces the search statement and argument dictionary to be executed
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For example, ``cursor.execute(*_build_search(query, weights))``
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"""Construct search statment for db execution.
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openstax/cnx-archive | cnxarchive/search.py | search | def search(query, query_type=DEFAULT_QUERY_TYPE):
"""Search database using parsed query.
Executes a database search query from the given ``query``
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By default, the search results are ordered by weight.
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"""Search database using parsed query.
Executes a database search query from the given ``query``
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openstax/cnx-archive | cnxarchive/search.py | Query.fix_quotes | def fix_quotes(cls, query_string):
"""Heuristic attempt to fix unbalanced quotes in query_string."""
if query_string.count('"') % 2 == 0:
# no unbalanced quotes to fix
return query_string
fields = [] # contains what's matched by the regexp
# e.g. fields = ['sort... | python | def fix_quotes(cls, query_string):
"""Heuristic attempt to fix unbalanced quotes in query_string."""
if query_string.count('"') % 2 == 0:
# no unbalanced quotes to fix
return query_string
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openstax/cnx-archive | cnxarchive/search.py | Query.from_raw_query | def from_raw_query(cls, query_string):
"""Parse raw string to query.
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"""
try:
node_tree = grammar.parse(query_string)
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"""Parse raw string to query.
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"""
try:
node_tree = grammar.parse(query_string)
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openstax/cnx-archive | cnxarchive/search.py | QueryRecord.highlighted_abstract | def highlighted_abstract(self):
"""Highlight the found terms in the abstract text."""
abstract_terms = self.fields.get('abstract', [])
if abstract_terms:
sql = _read_sql_file('highlighted-abstract')
else:
sql = _read_sql_file('get-abstract')
arguments = {'... | python | def highlighted_abstract(self):
"""Highlight the found terms in the abstract text."""
abstract_terms = self.fields.get('abstract', [])
if abstract_terms:
sql = _read_sql_file('highlighted-abstract')
else:
sql = _read_sql_file('get-abstract')
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openstax/cnx-archive | cnxarchive/search.py | QueryRecord.highlighted_fulltext | def highlighted_fulltext(self):
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terms = self.fields.get('fulltext', [])
if not terms:
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arguments = {'id': self['id'],
'query': ' & '.join(terms),
}
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"""Highlight the found terms in the fulltext."""
terms = self.fields.get('fulltext', [])
if not terms:
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ZELLMECHANIK-DRESDEN/dclab | dclab/external/statsmodels/nonparametric/kernel_density.py | KDEMultivariate.pdf | def pdf(self, data_predict=None):
r"""
Evaluate the probability density function.
Parameters
----------
data_predict: array_like, optional
Points to evaluate at. If unspecified, the training data is used.
Returns
-------
pdf_est: array_like
... | python | def pdf(self, data_predict=None):
r"""
Evaluate the probability density function.
Parameters
----------
data_predict: array_like, optional
Points to evaluate at. If unspecified, the training data is used.
Returns
-------
pdf_est: array_like
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xenon-middleware/pyxenon | xenon/compat.py | find_xenon_grpc_jar | def find_xenon_grpc_jar():
"""Find the Xenon-GRPC jar-file, windows version."""
prefix = Path(sys.prefix)
locations = [
prefix / 'lib',
prefix / 'local' / 'lib'
]
for location in locations:
jar_file = location / 'xenon-grpc-{}-all.jar'.format(
xenon_grpc_ver... | python | def find_xenon_grpc_jar():
"""Find the Xenon-GRPC jar-file, windows version."""
prefix = Path(sys.prefix)
locations = [
prefix / 'lib',
prefix / 'local' / 'lib'
]
for location in locations:
jar_file = location / 'xenon-grpc-{}-all.jar'.format(
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xenon-middleware/pyxenon | xenon/compat.py | kill_process | def kill_process(process):
"""Kill the process group associated with the given process. (posix)"""
logger = logging.getLogger('xenon')
logger.info('Terminating Xenon-GRPC server.')
os.kill(process.pid, signal.SIGINT)
process.wait() | python | def kill_process(process):
"""Kill the process group associated with the given process. (posix)"""
logger = logging.getLogger('xenon')
logger.info('Terminating Xenon-GRPC server.')
os.kill(process.pid, signal.SIGINT)
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xenon-middleware/pyxenon | xenon/compat.py | start_xenon_server | def start_xenon_server(port=50051, disable_tls=False):
"""Start the server."""
jar_file = find_xenon_grpc_jar()
if not jar_file:
raise RuntimeError("Could not find 'xenon-grpc' jar file.")
cmd = ['java', '-jar', jar_file, '-p', str(port)]
if not disable_tls:
crt_file, key_file = cr... | python | def start_xenon_server(port=50051, disable_tls=False):
"""Start the server."""
jar_file = find_xenon_grpc_jar()
if not jar_file:
raise RuntimeError("Could not find 'xenon-grpc' jar file.")
cmd = ['java', '-jar', jar_file, '-p', str(port)]
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simse/pymitv | pymitv/control.py | Control.send_keystrokes | def send_keystrokes(ip, keystrokes, wait=False):
"""Connects to TV and sends keystroke via HTTP."""
tv_url = 'http://{}:6095/controller?action=keyevent&keycode='.format(ip)
for keystroke in keystrokes:
if keystroke == 'wait' or wait is True:
time.sleep(0.7)
... | python | def send_keystrokes(ip, keystrokes, wait=False):
"""Connects to TV and sends keystroke via HTTP."""
tv_url = 'http://{}:6095/controller?action=keyevent&keycode='.format(ip)
for keystroke in keystrokes:
if keystroke == 'wait' or wait is True:
time.sleep(0.7)
... | [
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simse/pymitv | pymitv/control.py | Control.mute | def mute(ip):
"""Polyfill for muting the TV."""
tv_url = 'http://{}:6095/controller?action=keyevent&keycode='.format(ip)
count = 0
while count > 30:
count = count + 1
request = requests.get(tv_url + 'volumedown')
if request.status_code != 20... | python | def mute(ip):
"""Polyfill for muting the TV."""
tv_url = 'http://{}:6095/controller?action=keyevent&keycode='.format(ip)
count = 0
while count > 30:
count = count + 1
request = requests.get(tv_url + 'volumedown')
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openstax/cnx-archive | cnxarchive/views/in_book_search.py | in_book_search | def in_book_search(request):
"""Full text, in-book search."""
results = {}
args = request.matchdict
ident_hash = args['ident_hash']
args['search_term'] = request.params.get('q', '')
query_type = request.params.get('query_type', '')
combiner = ''
if query_type:
if query_type.low... | python | def in_book_search(request):
"""Full text, in-book search."""
results = {}
args = request.matchdict
ident_hash = args['ident_hash']
args['search_term'] = request.params.get('q', '')
query_type = request.params.get('query_type', '')
combiner = ''
if query_type:
if query_type.low... | [
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openstax/cnx-archive | cnxarchive/views/in_book_search.py | in_book_search_highlighted_results | def in_book_search_highlighted_results(request):
"""In-book search - returns a highlighted version of the HTML."""
results = {}
args = request.matchdict
ident_hash = args['ident_hash']
page_ident_hash = args['page_ident_hash']
try:
page_uuid, _ = split_ident_hash(page_ident_hash)
e... | python | def in_book_search_highlighted_results(request):
"""In-book search - returns a highlighted version of the HTML."""
results = {}
args = request.matchdict
ident_hash = args['ident_hash']
page_ident_hash = args['page_ident_hash']
try:
page_uuid, _ = split_ident_hash(page_ident_hash)
e... | [
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ZELLMECHANIK-DRESDEN/dclab | dclab/external/statsmodels/nonparametric/_kernel_base.py | _adjust_shape | def _adjust_shape(dat, k_vars):
""" Returns an array of shape (nobs, k_vars) for use with `gpke`."""
dat = np.asarray(dat)
if dat.ndim > 2:
dat = np.squeeze(dat)
if dat.ndim == 1 and k_vars > 1: # one obs many vars
nobs = 1
elif dat.ndim == 1 and k_vars == 1: # one obs one var
... | python | def _adjust_shape(dat, k_vars):
""" Returns an array of shape (nobs, k_vars) for use with `gpke`."""
dat = np.asarray(dat)
if dat.ndim > 2:
dat = np.squeeze(dat)
if dat.ndim == 1 and k_vars > 1: # one obs many vars
nobs = 1
elif dat.ndim == 1 and k_vars == 1: # one obs one var
... | [
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ZELLMECHANIK-DRESDEN/dclab | dclab/external/statsmodels/nonparametric/_kernel_base.py | gpke | def gpke(bw, data, data_predict, var_type, ckertype='gaussian',
okertype='wangryzin', ukertype='aitchisonaitken', tosum=True):
r"""
Returns the non-normalized Generalized Product Kernel Estimator
Parameters
----------
bw: 1-D ndarray
The user-specified bandwidth parameters.
dat... | python | def gpke(bw, data, data_predict, var_type, ckertype='gaussian',
okertype='wangryzin', ukertype='aitchisonaitken', tosum=True):
r"""
Returns the non-normalized Generalized Product Kernel Estimator
Parameters
----------
bw: 1-D ndarray
The user-specified bandwidth parameters.
dat... | [
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data: 1D or 2-D ndarray
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ZELLMECHANIK-DRESDEN/dclab | dclab/external/statsmodels/nonparametric/_kernel_base.py | GenericKDE._compute_bw | def _compute_bw(self, bw):
"""
Computes the bandwidth of the data.
Parameters
----------
bw: array_like or str
If array_like: user-specified bandwidth.
If a string, should be one of:
- cv_ml: cross validation maximum likelihood
... | python | def _compute_bw(self, bw):
"""
Computes the bandwidth of the data.
Parameters
----------
bw: array_like or str
If array_like: user-specified bandwidth.
If a string, should be one of:
- cv_ml: cross validation maximum likelihood
... | [
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bw: array_like or str
If array_like: user-specified bandwidth.
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ZELLMECHANIK-DRESDEN/dclab | dclab/external/statsmodels/nonparametric/_kernel_base.py | GenericKDE._set_defaults | def _set_defaults(self, defaults):
"""Sets the default values for the efficient estimation"""
self.n_res = defaults.n_res
self.n_sub = defaults.n_sub
self.randomize = defaults.randomize
self.return_median = defaults.return_median
self.efficient = defaults.efficient
... | python | def _set_defaults(self, defaults):
"""Sets the default values for the efficient estimation"""
self.n_res = defaults.n_res
self.n_sub = defaults.n_sub
self.randomize = defaults.randomize
self.return_median = defaults.return_median
self.efficient = defaults.efficient
... | [
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mhostetter/nhl | docs/conf.py | get_version | def get_version():
"""Return package version from setup.cfg"""
config = RawConfigParser()
config.read(os.path.join('..', 'setup.cfg'))
return config.get('metadata', 'version') | python | def get_version():
"""Return package version from setup.cfg"""
config = RawConfigParser()
config.read(os.path.join('..', 'setup.cfg'))
return config.get('metadata', 'version') | [
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