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sonyxperiadev/pygerrit | pygerrit/stream.py | GerritStream.run | def run(self):
""" Listen to the stream and send events to the client. """
channel = self._ssh_client.get_transport().open_session()
self._channel = channel
channel.exec_command("gerrit stream-events")
stdout = channel.makefile()
stderr = channel.makefile_stderr()
... | python | def run(self):
""" Listen to the stream and send events to the client. """
channel = self._ssh_client.get_transport().open_session()
self._channel = channel
channel.exec_command("gerrit stream-events")
stdout = channel.makefile()
stderr = channel.makefile_stderr()
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sonyxperiadev/pygerrit | pygerrit/client.py | GerritClient.run_command | def run_command(self, command):
""" Run a command.
:arg str command: The command to run.
:Return: The result as a string.
:Raises: `ValueError` if `command` is not a string.
"""
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sonyxperiadev/pygerrit | pygerrit/client.py | GerritClient.query | def query(self, term):
""" Run a query.
:arg str term: The query term to run.
:Returns: A list of results as :class:`pygerrit.models.Change` objects.
:Raises: `ValueError` if `term` is not a string.
"""
results = []
command = ["query", "--current-patch-set", "... | python | def query(self, term):
""" Run a query.
:arg str term: The query term to run.
:Returns: A list of results as :class:`pygerrit.models.Change` objects.
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sonyxperiadev/pygerrit | pygerrit/client.py | GerritClient.start_event_stream | def start_event_stream(self):
""" Start streaming events from `gerrit stream-events`. """
if not self._stream:
self._stream = GerritStream(self, ssh_client=self._ssh_client)
self._stream.start() | python | def start_event_stream(self):
""" Start streaming events from `gerrit stream-events`. """
if not self._stream:
self._stream = GerritStream(self, ssh_client=self._ssh_client)
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sonyxperiadev/pygerrit | pygerrit/client.py | GerritClient.stop_event_stream | def stop_event_stream(self):
""" Stop streaming events from `gerrit stream-events`."""
if self._stream:
self._stream.stop()
self._stream.join()
self._stream = None
with self._events.mutex:
self._events.queue.clear() | python | def stop_event_stream(self):
""" Stop streaming events from `gerrit stream-events`."""
if self._stream:
self._stream.stop()
self._stream.join()
self._stream = None
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sonyxperiadev/pygerrit | pygerrit/client.py | GerritClient.get_event | def get_event(self, block=True, timeout=None):
""" Get the next event from the queue.
:arg boolean block: Set to True to block if no event is available.
:arg seconds timeout: Timeout to wait if no event is available.
:Returns: The next event as a :class:`pygerrit.events.GerritEvent`
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""" Get the next event from the queue.
:arg boolean block: Set to True to block if no event is available.
:arg seconds timeout: Timeout to wait if no event is available.
:Returns: The next event as a :class:`pygerrit.events.GerritEvent`
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sonyxperiadev/pygerrit | pygerrit/client.py | GerritClient.put_event | def put_event(self, data):
""" Create event from `data` and add it to the queue.
:arg json data: The JSON data from which to create the event.
:Raises: :class:`pygerrit.error.GerritError` if the queue is full, or
the factory could not create the event.
"""
try:
... | python | def put_event(self, data):
""" Create event from `data` and add it to the queue.
:arg json data: The JSON data from which to create the event.
:Raises: :class:`pygerrit.error.GerritError` if the queue is full, or
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sonyxperiadev/pygerrit | pygerrit/ssh.py | _extract_version | def _extract_version(version_string, pattern):
""" Extract the version from `version_string` using `pattern`.
Return the version as a string, with leading/trailing whitespace
stripped.
"""
if version_string:
match = pattern.match(version_string.strip())
if match:
return... | python | def _extract_version(version_string, pattern):
""" Extract the version from `version_string` using `pattern`.
Return the version as a string, with leading/trailing whitespace
stripped.
"""
if version_string:
match = pattern.match(version_string.strip())
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sonyxperiadev/pygerrit | pygerrit/ssh.py | GerritSSHClient._configure | def _configure(self):
""" Configure the ssh parameters from the config file. """
configfile = expanduser("~/.ssh/config")
if not isfile(configfile):
raise GerritError("ssh config file '%s' does not exist" %
configfile)
config = SSHConfig()
... | python | def _configure(self):
""" Configure the ssh parameters from the config file. """
configfile = expanduser("~/.ssh/config")
if not isfile(configfile):
raise GerritError("ssh config file '%s' does not exist" %
configfile)
config = SSHConfig()
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sonyxperiadev/pygerrit | pygerrit/ssh.py | GerritSSHClient._do_connect | def _do_connect(self):
""" Connect to the remote. """
self.load_system_host_keys()
if self.username is None or self.port is None:
self._configure()
try:
self.connect(hostname=self.hostname,
port=self.port,
username... | python | def _do_connect(self):
""" Connect to the remote. """
self.load_system_host_keys()
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sonyxperiadev/pygerrit | pygerrit/ssh.py | GerritSSHClient._connect | def _connect(self):
""" Connect to the remote if not already connected. """
if not self.connected.is_set():
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# Another thread may have connected while we were
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""" Connect to the remote if not already connected. """
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sonyxperiadev/pygerrit | pygerrit/ssh.py | GerritSSHClient.get_remote_version | def get_remote_version(self):
""" Return the version of the remote Gerrit server. """
if self.remote_version is None:
result = self.run_gerrit_command("version")
version_string = result.stdout.read()
pattern = re.compile(r'^gerrit version (.*)$')
self.remo... | python | def get_remote_version(self):
""" Return the version of the remote Gerrit server. """
if self.remote_version is None:
result = self.run_gerrit_command("version")
version_string = result.stdout.read()
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sonyxperiadev/pygerrit | pygerrit/ssh.py | GerritSSHClient.run_gerrit_command | def run_gerrit_command(self, command):
""" Run the given command.
Make sure we're connected to the remote server, and run `command`.
Return the results as a `GerritSSHCommandResult`.
Raise `ValueError` if `command` is not a string, or `GerritError` if
command execution fails.
... | python | def run_gerrit_command(self, command):
""" Run the given command.
Make sure we're connected to the remote server, and run `command`.
Return the results as a `GerritSSHCommandResult`.
Raise `ValueError` if `command` is not a string, or `GerritError` if
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sonyxperiadev/pygerrit | pygerrit/events.py | GerritEventFactory.register | def register(cls, name):
""" Decorator to register the event identified by `name`.
Return the decorated class.
Raise GerritError if the event is already registered.
"""
def decorate(klazz):
""" Decorator. """
if name in cls._events:
rai... | python | def register(cls, name):
""" Decorator to register the event identified by `name`.
Return the decorated class.
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"""
def decorate(klazz):
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sonyxperiadev/pygerrit | pygerrit/events.py | GerritEventFactory.create | def create(cls, data):
""" Create a new event instance.
Return an instance of the `GerritEvent` subclass after converting
`data` to json.
Raise GerritError if json parsed from `data` does not contain a `type`
key.
"""
try:
json_data = json.loads(dat... | python | def create(cls, data):
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Return an instance of the `GerritEvent` subclass after converting
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sonyxperiadev/pygerrit | pygerrit/rest/__init__.py | _decode_response | def _decode_response(response):
""" Strip off Gerrit's magic prefix and decode a response.
:returns:
Decoded JSON content as a dict, or raw text if content could not be
decoded as JSON.
:raises:
requests.HTTPError if the response contains an HTTP error status code.
"""
con... | python | def _decode_response(response):
""" Strip off Gerrit's magic prefix and decode a response.
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Decoded JSON content as a dict, or raw text if content could not be
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sonyxperiadev/pygerrit | pygerrit/rest/__init__.py | GerritRestAPI.put | def put(self, endpoint, **kwargs):
""" Send HTTP PUT to the endpoint.
:arg str endpoint: The endpoint to send to.
:returns:
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:raises:
requests.RequestException on timeout or connection error.
"""
kwargs.update(self.kwargs.co... | python | def put(self, endpoint, **kwargs):
""" Send HTTP PUT to the endpoint.
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JSON decoded result.
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:returns:
JSON decoded result.
:raises:
requests.RequestException on timeout or connection error.
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sonyxperiadev/pygerrit | pygerrit/rest/__init__.py | GerritRestAPI.review | def review(self, change_id, revision, review):
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:arg str revision: The revision.
:arg str review: The review details as a :class:`GerritReview`.
:returns:
JSON decoded result.
:raises:
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""" Submit a review.
:arg str change_id: The change ID.
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sonyxperiadev/pygerrit | pygerrit/rest/__init__.py | GerritReview.add_comments | def add_comments(self, comments):
""" Add inline comments.
:arg dict comments: Comments to add.
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add_comments([{'filename': 'Makefile',
'line': 10,
'message': 'inline message'}])
add_comments([{'filename': '... | python | def add_comments(self, comments):
""" Add inline comments.
:arg dict comments: Comments to add.
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SiriDB/siridb-connector | siridb/connector/lib/protocol.py | _SiriDBProtocol.connection_made | def connection_made(self, transport):
'''
override asyncio.Protocol
'''
self._connected = True
self.transport = transport
self.remote_ip, self.port = transport.get_extra_info('peername')[:2]
logging.debug(
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'''
override asyncio.Protocol
'''
self._connected = True
self.transport = transport
self.remote_ip, self.port = transport.get_extra_info('peername')[:2]
logging.debug(
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SiriDB/siridb-connector | siridb/connector/lib/protocol.py | _SiriDBProtocol.connection_lost | def connection_lost(self, exc):
'''
override asyncio.Protocol
'''
self._connected = False
logging.debug(
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for pid, (future, task) in self._requests.items():
t... | python | def connection_lost(self, exc):
'''
override asyncio.Protocol
'''
self._connected = False
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SiriDB/siridb-connector | siridb/connector/lib/protocol.py | _SiriDBProtocol.data_received | def data_received(self, data):
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size = len(self._buffered_data)
if self._data_package is None:
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'''
override asyncio.Protocol
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self._buffered_data.extend(data)
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SiriDB/siridb-connector | siridb/connector/lib/protocol.py | _SiriDBInfoProtocol.connection_made | def connection_made(self, transport):
'''
override _SiriDBProtocol
'''
self.transport = transport
self.remote_ip, self.port = transport.get_extra_info('peername')[:2]
logging.debug(
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'''
override _SiriDBProtocol
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SiriDB/siridb-connector | siridb/connector/lib/connection.py | SiriDBConnection._register_server | def _register_server(self, server, timeout=30):
'''Register a new SiriDB Server.
This method is used by the SiriDB manage tool and should not be used
otherwise. Full access rights are required for this request.
'''
result = self._loop.run_until_complete(
self._protoc... | python | def _register_server(self, server, timeout=30):
'''Register a new SiriDB Server.
This method is used by the SiriDB manage tool and should not be used
otherwise. Full access rights are required for this request.
'''
result = self._loop.run_until_complete(
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SiriDB/siridb-connector | siridb/connector/lib/connection.py | SiriDBConnection._get_file | def _get_file(self, fn, timeout=30):
'''Request a SiriDB configuration file.
This method is used by the SiriDB manage tool and should not be used
otherwise. Full access rights are required for this request.
'''
msg = FILE_MAP.get(fn, None)
if msg is None:
rai... | python | def _get_file(self, fn, timeout=30):
'''Request a SiriDB configuration file.
This method is used by the SiriDB manage tool and should not be used
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'''
msg = FILE_MAP.get(fn, None)
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transitland/mapzen-geohash | mzgeohash/geohash.py | _bits_to_float | def _bits_to_float(bits, lower=-90.0, middle=0.0, upper=90.0):
"""Convert GeoHash bits to a float."""
for i in bits:
if i:
lower = middle
else:
upper = middle
middle = (upper + lower) / 2
return middle | python | def _bits_to_float(bits, lower=-90.0, middle=0.0, upper=90.0):
"""Convert GeoHash bits to a float."""
for i in bits:
if i:
lower = middle
else:
upper = middle
middle = (upper + lower) / 2
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transitland/mapzen-geohash | mzgeohash/geohash.py | _float_to_bits | def _float_to_bits(value, lower=-90.0, middle=0.0, upper=90.0, length=15):
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transitland/mapzen-geohash | mzgeohash/geohash.py | _geohash_to_bits | def _geohash_to_bits(value):
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ret = []
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"""Convert a GeoHash to a list of GeoHash bits."""
b = map(BASE32MAP.get, value)
ret = []
for i in b:
out = []
for z in range(5):
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transitland/mapzen-geohash | mzgeohash/geohash.py | _bits_to_geohash | def _bits_to_geohash(value):
"""Convert a list of GeoHash bits to a GeoHash."""
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# Convert binary to integer
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"""Convert a list of GeoHash bits to a GeoHash."""
ret = []
# Get 5 bits at a time
for i in (value[i:i+5] for i in xrange(0, len(value), 5)):
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transitland/mapzen-geohash | mzgeohash/geohash.py | decode | def decode(value):
"""Decode a geohash. Returns a (lon,lat) pair."""
assert value, "Invalid geohash: %s"%value
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bits = _geohash_to_bits(value)
# Unzip the GeoHash bits.
lon = bits[0::2]
lat = bits[1::2]
# Convert to lat/lon
return (
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"""Decode a geohash. Returns a (lon,lat) pair."""
assert value, "Invalid geohash: %s"%value
# Get the GeoHash bits
bits = _geohash_to_bits(value)
# Unzip the GeoHash bits.
lon = bits[0::2]
lat = bits[1::2]
# Convert to lat/lon
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transitland/mapzen-geohash | mzgeohash/geohash.py | encode | def encode(lonlat, length=12):
"""Encode a (lon,lat) pair to a GeoHash."""
assert len(lonlat) == 2, "Invalid lon/lat: %s"%lonlat
# Half the length for each component.
length /= 2
lon = _float_to_bits(lonlat[0], lower=-180.0, upper=180.0, length=length*5)
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"""Encode a (lon,lat) pair to a GeoHash."""
assert len(lonlat) == 2, "Invalid lon/lat: %s"%lonlat
# Half the length for each component.
length /= 2
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transitland/mapzen-geohash | mzgeohash/geohash.py | adjacent | def adjacent(geohash, direction):
"""Return the adjacent geohash for a given direction."""
# Based on an MIT licensed implementation by Chris Veness from:
# http://www.movable-type.co.uk/scripts/geohash.html
assert direction in 'nsew', "Invalid direction: %s"%direction
assert geohash, "Invalid geohash: %s"%... | python | def adjacent(geohash, direction):
"""Return the adjacent geohash for a given direction."""
# Based on an MIT licensed implementation by Chris Veness from:
# http://www.movable-type.co.uk/scripts/geohash.html
assert direction in 'nsew', "Invalid direction: %s"%direction
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SiLab-Bonn/pyBAR | pybar/run_manager.py | thunkify | def thunkify(thread_name=None, daemon=True, default_func=None):
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Taken from https://wiki.python.org/moin/PythonDecoratorLibrary.
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SiLab-Bonn/pyBAR | pybar/run_manager.py | set_event_when_keyboard_interrupt | def set_event_when_keyboard_interrupt(_lambda):
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Lambda function that points to Threading.Event() object
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SiLab-Bonn/pyBAR | pybar/run_manager.py | RunBase.run_id | def run_id(self):
'''Run name without whitespace
'''
s1 = re.sub('(.)([A-Z][a-z]+)', r'\1_\2', self.__class__.__name__)
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'''Run name without whitespace
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SiLab-Bonn/pyBAR | pybar/run_manager.py | RunBase.conf | def conf(self):
'''Configuration (namedtuple)
'''
conf = namedtuple('conf', field_names=self._conf.keys())
return conf(**self._conf) | python | def conf(self):
'''Configuration (namedtuple)
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SiLab-Bonn/pyBAR | pybar/run_manager.py | RunBase.run_conf | def run_conf(self):
'''Run configuration (namedtuple)
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run_conf = namedtuple('run_conf', field_names=self._run_conf.keys())
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'''Run configuration (namedtuple)
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SiLab-Bonn/pyBAR | pybar/run_manager.py | RunBase.default_run_conf | def default_run_conf(self):
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default_run_conf = namedtuple('default_run_conf', field_names=self._default_run_conf.keys())
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SiLab-Bonn/pyBAR | pybar/run_manager.py | RunBase._init | def _init(self, run_conf, run_number=None):
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self.stop_run.clear()
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SiLab-Bonn/pyBAR | pybar/run_manager.py | RunBase.connect_cancel | def connect_cancel(self, functions):
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SiLab-Bonn/pyBAR | pybar/run_manager.py | RunBase.handle_cancel | def handle_cancel(self, **kwargs):
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SiLab-Bonn/pyBAR | pybar/run_manager.py | RunBase.stop | def stop(self, msg=None):
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'''
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SiLab-Bonn/pyBAR | pybar/run_manager.py | RunBase.abort | def abort(self, msg=None):
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SiLab-Bonn/pyBAR | pybar/run_manager.py | RunManager.run_run | def run_run(self, run, conf=None, run_conf=None, use_thread=False, catch_exception=True):
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Parameters
----------
run : class, object
Run class or object.
run_conf : str, dict, file
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SiLab-Bonn/pyBAR | pybar/run_manager.py | RunManager.run_primlist | def run_primlist(self, primlist, skip_remaining=False):
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Parameters
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primlist : string
Filename of primlist.
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SiLab-Bonn/pyBAR | pybar/analysis/analysis.py | analyze_beam_spot | def analyze_beam_spot(scan_base, combine_n_readouts=1000, chunk_size=10000000, plot_occupancy_hists=False, output_pdf=None, output_file=None):
''' Determines the mean x and y beam spot position as a function of time. Therefore the data of a fixed number of read outs are combined ('combine_n_readouts'). The occupanc... | python | def analyze_beam_spot(scan_base, combine_n_readouts=1000, chunk_size=10000000, plot_occupancy_hists=False, output_pdf=None, output_file=None):
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SiLab-Bonn/pyBAR | pybar/analysis/analysis.py | analyze_event_rate | def analyze_event_rate(scan_base, combine_n_readouts=1000, time_line_absolute=True, output_pdf=None, output_file=None):
''' Determines the number of events as a function of time. Therefore the data of a fixed number of read outs are combined ('combine_n_readouts'). The number of events is taken from the meta data i... | python | def analyze_event_rate(scan_base, combine_n_readouts=1000, time_line_absolute=True, output_pdf=None, output_file=None):
''' Determines the number of events as a function of time. Therefore the data of a fixed number of read outs are combined ('combine_n_readouts'). The number of events is taken from the meta data i... | [
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SiLab-Bonn/pyBAR | pybar/analysis/analysis.py | analyse_n_cluster_per_event | def analyse_n_cluster_per_event(scan_base, include_no_cluster=False, time_line_absolute=True, combine_n_readouts=1000, chunk_size=10000000, plot_n_cluster_hists=False, output_pdf=None, output_file=None):
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SiLab-Bonn/pyBAR | pybar/analysis/analysis.py | select_hits_from_cluster_info | def select_hits_from_cluster_info(input_file_hits, output_file_hits, cluster_size_condition, n_cluster_condition, chunk_size=4000000):
''' Takes a hit table and stores only selected hits into a new table. The selection is done on an event base and events are selected if they have a certain number of cluster or clus... | python | def select_hits_from_cluster_info(input_file_hits, output_file_hits, cluster_size_condition, n_cluster_condition, chunk_size=4000000):
''' Takes a hit table and stores only selected hits into a new table. The selection is done on an event base and events are selected if they have a certain number of cluster or clus... | [
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SiLab-Bonn/pyBAR | pybar/analysis/analysis.py | select_hits | def select_hits(input_file_hits, output_file_hits, condition=None, cluster_size_condition=None, n_cluster_condition=None, chunk_size=5000000):
''' Takes a hit table and stores only selected hits into a new table. The selection of hits is done with a numexp string. Only if
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SiLab-Bonn/pyBAR | pybar/analysis/analysis.py | analyze_cluster_size_per_scan_parameter | def analyze_cluster_size_per_scan_parameter(input_file_hits, output_file_cluster_size, parameter='GDAC', max_chunk_size=10000000, overwrite_output_files=False, output_pdf=None):
''' This method takes multiple hit files and determines the cluster size for different scan parameter values of
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-----... | python | def analyze_cluster_size_per_scan_parameter(input_file_hits, output_file_cluster_size, parameter='GDAC', max_chunk_size=10000000, overwrite_output_files=False, output_pdf=None):
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SiLab-Bonn/pyBAR | pybar/analysis/analysis.py | histogram_cluster_table | def histogram_cluster_table(analyzed_data_file, output_file, chunk_size=10000000):
'''Reads in the cluster info table in chunks and histograms the seed pixels into one occupancy array.
The 3rd dimension of the occupancy array is the number of different scan parameters used
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ana... | python | def histogram_cluster_table(analyzed_data_file, output_file, chunk_size=10000000):
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SiLab-Bonn/pyBAR | pybar/analysis/analysis.py | analyze_hits_per_scan_parameter | def analyze_hits_per_scan_parameter(analyze_data, scan_parameters=None, chunk_size=50000):
'''Takes the hit table and analyzes the hits per scan parameter
Parameters
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SiLab-Bonn/pyBAR | pybar/scans/calibrate_plsr_dac_transient.py | interpret_data_from_tektronix | def interpret_data_from_tektronix(preamble, data):
''' Interprets raw data from Tektronix
returns: lists of x, y values in seconds/volt'''
# Y mode ("WFMPRE:PT_FMT"):
# Xn = XZEro + XINcr (n - PT_Off)
# Yn = YZEro + YMUlt (yn - YOFf)
voltage = np.array(data, dtype=np.float)
meta_data = pream... | python | def interpret_data_from_tektronix(preamble, data):
''' Interprets raw data from Tektronix
returns: lists of x, y values in seconds/volt'''
# Y mode ("WFMPRE:PT_FMT"):
# Xn = XZEro + XINcr (n - PT_Off)
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SiLab-Bonn/pyBAR | pybar/fei4/register_utils.py | read_chip_sn | def read_chip_sn(self):
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----
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Content | reserved | wafer number | chip number
'''
commands = []
commands.extend(self.register.get_commands("ConfMode"))
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Bits [MSB-LSB] | [15] | [14-6] | [5-0]
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SiLab-Bonn/pyBAR | pybar/fei4/register_utils.py | read_global_register | def read_global_register(self, name, overwrite_config=False):
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name : register name
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SiLab-Bonn/pyBAR | pybar/fei4/register_utils.py | read_pixel_register | def read_pixel_register(self, pix_regs=None, dcs=range(40), overwrite_config=False):
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SiLab-Bonn/pyBAR | pybar/fei4/register_utils.py | is_fe_ready | def is_fe_ready(self):
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value : bool
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SiLab-Bonn/pyBAR | pybar/fei4/register_utils.py | invert_pixel_mask | def invert_pixel_mask(mask):
'''Invert pixel mask (0->1, 1(and greater)->0).
Parameters
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mask : array-like
Mask.
Returns
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inverted_mask : array-like
Inverted Mask.
'''
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mask : array-like
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SiLab-Bonn/pyBAR | pybar/fei4/register_utils.py | make_pixel_mask | def make_pixel_mask(steps, shift, default=0, value=1, enable_columns=None, mask=None):
'''Generate pixel mask.
Parameters
----------
steps : int
Number of mask steps, e.g. steps=3 (every third pixel is enabled), steps=336 (one pixel per column), steps=672 (one pixel per double column).
... | python | def make_pixel_mask(steps, shift, default=0, value=1, enable_columns=None, mask=None):
'''Generate pixel mask.
Parameters
----------
steps : int
Number of mask steps, e.g. steps=3 (every third pixel is enabled), steps=336 (one pixel per column), steps=672 (one pixel per double column).
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SiLab-Bonn/pyBAR | pybar/fei4/register_utils.py | make_pixel_mask_from_col_row | def make_pixel_mask_from_col_row(column, row, default=0, value=1):
'''Generate mask from column and row lists
Parameters
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column : iterable, int
List of colums values.
row : iterable, int
List of row values.
default : int
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'''Generate mask from column and row lists
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----------
column : iterable, int
List of colums values.
row : iterable, int
List of row values.
default : int
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SiLab-Bonn/pyBAR | pybar/fei4/register_utils.py | make_box_pixel_mask_from_col_row | def make_box_pixel_mask_from_col_row(column, row, default=0, value=1):
'''Generate box shaped mask from column and row lists. Takes the minimum and maximum value from each list.
Parameters
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column : iterable, int
List of colums values.
row : iterable, int
List of r... | python | def make_box_pixel_mask_from_col_row(column, row, default=0, value=1):
'''Generate box shaped mask from column and row lists. Takes the minimum and maximum value from each list.
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column : iterable, int
List of colums values.
row : iterable, int
List of r... | [
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SiLab-Bonn/pyBAR | pybar/fei4/register_utils.py | make_xtalk_mask | def make_xtalk_mask(mask):
"""
Generate xtalk mask (row - 1, row + 1) from pixel mask.
Parameters
----------
mask : ndarray
Pixel mask.
Returns
-------
ndarray
Xtalk mask.
Example
-------
Input:
[[1 0 0 0 0 0 1 0 0 0 ... 0 0 0 0 1 0 0 0... | python | def make_xtalk_mask(mask):
"""
Generate xtalk mask (row - 1, row + 1) from pixel mask.
Parameters
----------
mask : ndarray
Pixel mask.
Returns
-------
ndarray
Xtalk mask.
Example
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SiLab-Bonn/pyBAR | pybar/fei4/register_utils.py | make_checkerboard_mask | def make_checkerboard_mask(column_distance, row_distance, column_offset=0, row_offset=0, default=0, value=1):
"""
Generate chessboard/checkerboard mask.
Parameters
----------
column_distance : int
Column distance of the enabled pixels.
row_distance : int
Row distance of... | python | def make_checkerboard_mask(column_distance, row_distance, column_offset=0, row_offset=0, default=0, value=1):
"""
Generate chessboard/checkerboard mask.
Parameters
----------
column_distance : int
Column distance of the enabled pixels.
row_distance : int
Row distance of... | [
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SiLab-Bonn/pyBAR | pybar/fei4/register_utils.py | scan_loop | def scan_loop(self, command, repeat_command=100, use_delay=True, additional_delay=0, mask_steps=3, enable_mask_steps=None, enable_double_columns=None, same_mask_for_all_dc=False, fast_dc_loop=True, bol_function=None, eol_function=None, digital_injection=False, enable_shift_masks=None, disable_shift_masks=None, restore_... | python | def scan_loop(self, command, repeat_command=100, use_delay=True, additional_delay=0, mask_steps=3, enable_mask_steps=None, enable_double_columns=None, same_mask_for_all_dc=False, fast_dc_loop=True, bol_function=None, eol_function=None, digital_injection=False, enable_shift_masks=None, disable_shift_masks=None, restore_... | [
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SiLab-Bonn/pyBAR | pybar/fei4/register_utils.py | FEI4RegisterUtils.reset_service_records | def reset_service_records(self):
'''Resetting Service Records
This will reset Service Record counters. This will also bring back alive some FE where the output FIFO is stuck (no data is coming out in run mode).
This should be only issued after power up and in the case of a stuck FIFO, other... | python | def reset_service_records(self):
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SiLab-Bonn/pyBAR | pybar/fei4/register_utils.py | FEI4RegisterUtils.reset_bunch_counter | def reset_bunch_counter(self):
'''Resetting Bunch Counter
'''
logging.info('Resetting Bunch Counter')
commands = []
commands.extend(self.register.get_commands("RunMode"))
commands.extend(self.register.get_commands("BCR"))
self.send_commands(commands)
... | python | def reset_bunch_counter(self):
'''Resetting Bunch Counter
'''
logging.info('Resetting Bunch Counter')
commands = []
commands.extend(self.register.get_commands("RunMode"))
commands.extend(self.register.get_commands("BCR"))
self.send_commands(commands)
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SiLab-Bonn/pyBAR | pybar/analysis/analysis_utils.py | generate_threshold_mask | def generate_threshold_mask(hist):
'''Masking array elements when equal 0.0 or greater than 10 times the median
Parameters
----------
hist : array_like
Input data.
Returns
-------
masked array
Returns copy of the array with masked elements.
'''
masked_array = np.ma.... | python | def generate_threshold_mask(hist):
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----------
hist : array_like
Input data.
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-------
masked array
Returns copy of the array with masked elements.
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SiLab-Bonn/pyBAR | pybar/analysis/analysis_utils.py | unique_row | def unique_row(array, use_columns=None, selected_columns_only=False):
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SiLab-Bonn/pyBAR | pybar/analysis/analysis_utils.py | get_ranges_from_array | def get_ranges_from_array(arr, append_last=True):
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arr : array like
append_last: bool
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Returns
... | python | def get_ranges_from_array(arr, append_last=True):
'''Takes an array and calculates ranges [start, stop[. The last range end is none to keep the same length.
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arr : array like
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SiLab-Bonn/pyBAR | pybar/analysis/analysis_utils.py | in1d_sorted | def in1d_sorted(ar1, ar2):
"""
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"""
if ar1.shape[0] == 0 or ar2.shape[0] == 0: # check for empty arrays to avoid crash
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inds[inds == len(ar2)] = 0
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"""
Does the same than np.in1d but uses the fact that ar1 and ar2 are sorted. Is therefore much faster.
"""
if ar1.shape[0] == 0 or ar2.shape[0] == 0: # check for empty arrays to avoid crash
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SiLab-Bonn/pyBAR | pybar/analysis/analysis_utils.py | central_difference | def central_difference(x, y):
'''Returns the dy/dx(x) via central difference method
Parameters
----------
x : array like
y : array like
Returns
-------
dy/dx : array like
'''
if (len(x) != len(y)):
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z1 = np.hstack((y... | python | def central_difference(x, y):
'''Returns the dy/dx(x) via central difference method
Parameters
----------
x : array like
y : array like
Returns
-------
dy/dx : array like
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SiLab-Bonn/pyBAR | pybar/analysis/analysis_utils.py | get_profile_histogram | def get_profile_histogram(x, y, n_bins=100):
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SiLab-Bonn/pyBAR | pybar/analysis/analysis_utils.py | get_rate_normalization | def get_rate_normalization(hit_file, parameter, reference='event', cluster_file=None, plot=False, chunk_size=500000):
''' Takes different hit files (hit_files), extracts the number of events or the scan time (reference) per scan parameter (parameter)
and returns an array with a normalization factor. This normal... | python | def get_rate_normalization(hit_file, parameter, reference='event', cluster_file=None, plot=False, chunk_size=500000):
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SiLab-Bonn/pyBAR | pybar/analysis/analysis_utils.py | get_parameter_value_from_file_names | def get_parameter_value_from_file_names(files, parameters=None, unique=False, sort=True):
"""
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SiLab-Bonn/pyBAR | pybar/analysis/analysis_utils.py | get_data_file_names_from_scan_base | def get_data_file_names_from_scan_base(scan_base, filter_str=['_analyzed.h5', '_interpreted.h5', '_cut.h5', '_result.h5', '_hists.h5'], sort_by_time=True, meta_data_v2=True):
"""
Generate a list of .h5 files which have a similar file name.
Parameters
----------
scan_base : list, string
List... | python | def get_data_file_names_from_scan_base(scan_base, filter_str=['_analyzed.h5', '_interpreted.h5', '_cut.h5', '_result.h5', '_hists.h5'], sort_by_time=True, meta_data_v2=True):
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Generate a list of .h5 files which have a similar file name.
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scan_base : list, string
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SiLab-Bonn/pyBAR | pybar/analysis/analysis_utils.py | get_parameter_from_files | def get_parameter_from_files(files, parameters=None, unique=False, sort=True):
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SiLab-Bonn/pyBAR | pybar/analysis/analysis_utils.py | check_parameter_similarity | def check_parameter_similarity(files_dict):
"""
Checks if the parameter names of all files are similar. Takes the dictionary from get_parameter_from_files output as input.
"""
try:
parameter_names = files_dict.itervalues().next().keys() # get the parameter names of the first file, to check if ... | python | def check_parameter_similarity(files_dict):
"""
Checks if the parameter names of all files are similar. Takes the dictionary from get_parameter_from_files output as input.
"""
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SiLab-Bonn/pyBAR | pybar/analysis/analysis_utils.py | combine_meta_data | def combine_meta_data(files_dict, meta_data_v2=True):
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----------
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Takes the dict of hdf5 files and combines their meta data tables into one new numpy record array.
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SiLab-Bonn/pyBAR | pybar/analysis/analysis_utils.py | smooth_differentiation | def smooth_differentiation(x, y, weigths=None, order=5, smoothness=3, derivation=1):
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Parameters
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x : array like
y : array like
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dy/dx : array like
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'''Returns the dy/dx(x) with the fit and differentiation of a spline curve
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x : array like
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dy/dx : array like
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SiLab-Bonn/pyBAR | pybar/analysis/analysis_utils.py | reduce_sorted_to_intersect | def reduce_sorted_to_intersect(ar1, ar2):
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ar1 : (M,) array_like
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ar2 : array_like
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Returns
-------
ar1, ar1 : ndarray, ndarray
The ... | python | def reduce_sorted_to_intersect(ar1, ar2):
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SiLab-Bonn/pyBAR | pybar/analysis/analysis_utils.py | get_not_unique_values | def get_not_unique_values(array):
'''Returns the values that appear at least twice in array.
Parameters
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array : array like
Returns
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numpy.array
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return np.unique(s) | python | def get_not_unique_values(array):
'''Returns the values that appear at least twice in array.
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array : array like
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SiLab-Bonn/pyBAR | pybar/analysis/analysis_utils.py | get_meta_data_index_at_scan_parameter | def get_meta_data_index_at_scan_parameter(meta_data_array, scan_parameter_name):
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Parameters
----------
meta_data_array : numpy.recordarray
scan_parameter_name : string
Returns
-------
numpy.n... | python | def get_meta_data_index_at_scan_parameter(meta_data_array, scan_parameter_name):
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meta_data_array : numpy.recordarray
scan_parameter_name : string
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SiLab-Bonn/pyBAR | pybar/analysis/analysis_utils.py | select_hits | def select_hits(hits_array, condition=None):
'''Selects the hits with condition.
E.g.: condition = 'rel_BCID == 7 & event_number < 1000'
Parameters
----------
hits_array : numpy.array
condition : string
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hits_array : numpy.array
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SiLab-Bonn/pyBAR | pybar/analysis/analysis_utils.py | get_hits_in_events | def get_hits_in_events(hits_array, events, assume_sorted=True, condition=None):
'''Selects the hits that occurred in events and optional selection criterion.
If a event range can be defined use the get_data_in_event_range function. It is much faster.
Parameters
----------
hits_array : numpy.arr... | python | def get_hits_in_events(hits_array, events, assume_sorted=True, condition=None):
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SiLab-Bonn/pyBAR | pybar/analysis/analysis_utils.py | get_hits_of_scan_parameter | def get_hits_of_scan_parameter(input_file_hits, scan_parameters=None, try_speedup=False, chunk_size=10000000):
'''Takes the hit table of a hdf5 file and returns hits in chunks for each unique combination of scan_parameters.
Yields the hits in chunks, since they usually do not fit into memory.
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... | python | def get_hits_of_scan_parameter(input_file_hits, scan_parameters=None, try_speedup=False, chunk_size=10000000):
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SiLab-Bonn/pyBAR | pybar/analysis/analysis_utils.py | get_data_in_event_range | def get_data_in_event_range(array, event_start=None, event_stop=None, assume_sorted=True):
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array : numpy.array
event_start : int, None
event_stop : int, None
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SiLab-Bonn/pyBAR | pybar/analysis/analysis_utils.py | write_hits_in_events | def write_hits_in_events(hit_table_in, hit_table_out, events, start_hit_word=0, chunk_size=5000000, condition=None):
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SiLab-Bonn/pyBAR | pybar/analysis/analysis_utils.py | write_hits_in_event_range | def write_hits_in_event_range(hit_table_in, hit_table_out, event_start=None, event_stop=None, start_hit_word=0, chunk_size=5000000, condition=None):
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SiLab-Bonn/pyBAR | pybar/analysis/analysis_utils.py | get_events_with_n_cluster | def get_events_with_n_cluster(event_number, condition='n_cluster==1'):
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event_number : numpy.array
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SiLab-Bonn/pyBAR | pybar/analysis/analysis_utils.py | get_events_with_cluster_size | def get_events_with_cluster_size(event_number, cluster_size, condition='cluster_size==1'):
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event_number : numpy.array
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SiLab-Bonn/pyBAR | pybar/analysis/analysis_utils.py | get_events_with_error_code | def get_events_with_error_code(event_number, event_status, select_mask=0b1111111111111111, condition=0b0000000000000000):
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SiLab-Bonn/pyBAR | pybar/analysis/analysis_utils.py | get_scan_parameter | def get_scan_parameter(meta_data_array, unique=True):
'''Takes the numpy meta data array and returns the different scan parameter settings and the name aligned in a dictionary
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SiLab-Bonn/pyBAR | pybar/analysis/analysis_utils.py | get_scan_parameters_table_from_meta_data | def get_scan_parameters_table_from_meta_data(meta_data_array, scan_parameters=None):
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SiLab-Bonn/pyBAR | pybar/analysis/analysis_utils.py | get_scan_parameters_index | def get_scan_parameters_index(scan_parameter):
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The table with the scan parameters.
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SiLab-Bonn/pyBAR | pybar/analysis/analysis_utils.py | get_unique_scan_parameter_combinations | def get_unique_scan_parameter_combinations(meta_data_array, scan_parameters=None, scan_parameter_columns_only=False):
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SiLab-Bonn/pyBAR | pybar/analysis/analysis_utils.py | data_aligned_at_events | def data_aligned_at_events(table, start_event_number=None, stop_event_number=None, start_index=None, stop_index=None, chunk_size=10000000, try_speedup=False, first_event_aligned=True, fail_on_missing_events=True):
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SiLab-Bonn/pyBAR | pybar/analysis/analysis_utils.py | select_good_pixel_region | def select_good_pixel_region(hits, col_span, row_span, min_cut_threshold=0.2, max_cut_threshold=2.0):
'''Takes the hit array and masks all pixels with a certain occupancy.
Parameters
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hits : array like
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min_cut_threshold : float
... | python | def select_good_pixel_region(hits, col_span, row_span, min_cut_threshold=0.2, max_cut_threshold=2.0):
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"with",
"a",
"certain",
"occupancy",
"."
] | train | https://github.com/SiLab-Bonn/pyBAR/blob/5ad95bbcd41cd358825823fb78f396cfce23593e/pybar/analysis/analysis_utils.py#L1323-L1353 |
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