partition stringclasses 3
values | func_name stringlengths 1 134 | docstring stringlengths 1 46.9k | path stringlengths 4 223 | original_string stringlengths 75 104k | code stringlengths 75 104k | docstring_tokens listlengths 1 1.97k | repo stringlengths 7 55 | language stringclasses 1
value | url stringlengths 87 315 | code_tokens listlengths 19 28.4k | sha stringlengths 40 40 |
|---|---|---|---|---|---|---|---|---|---|---|---|
test | tokenize | Convert a single string into a list of substrings
split along punctuation and word boundaries. Keep
whitespace intact by always attaching it to the
previous token.
Arguments:
----------
text : str
normalize_ascii : bool, perform some replacements
on non-ascii characters ... | ciseau/word_tokenizer.py | def tokenize(text, normalize_ascii=True):
"""
Convert a single string into a list of substrings
split along punctuation and word boundaries. Keep
whitespace intact by always attaching it to the
previous token.
Arguments:
----------
text : str
normalize_ascii : bool, perform ... | def tokenize(text, normalize_ascii=True):
"""
Convert a single string into a list of substrings
split along punctuation and word boundaries. Keep
whitespace intact by always attaching it to the
previous token.
Arguments:
----------
text : str
normalize_ascii : bool, perform ... | [
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"Keep",
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"intact",
"by",
"always",
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"."
] | JonathanRaiman/ciseau | python | https://github.com/JonathanRaiman/ciseau/blob/f72d1c82d85eeb3d3ac9fac17690041725402175/ciseau/word_tokenizer.py#L185-L260 | [
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"# 2. let's standardize the input text to ascii ... | f72d1c82d85eeb3d3ac9fac17690041725402175 |
test | main | Main command line interface. | keyrings/cryptfile/convert.py | def main(argv=None):
"""Main command line interface."""
if argv is None:
argv = sys.argv[1:]
cli = CommandLineTool()
try:
return cli.run(argv)
except KeyboardInterrupt:
print('Canceled')
return 3 | def main(argv=None):
"""Main command line interface."""
if argv is None:
argv = sys.argv[1:]
cli = CommandLineTool()
try:
return cli.run(argv)
except KeyboardInterrupt:
print('Canceled')
return 3 | [
"Main",
"command",
"line",
"interface",
"."
] | frispete/keyrings.cryptfile | python | https://github.com/frispete/keyrings.cryptfile/blob/cfa80d4848a5c3c0aeee41a954b2b120c80e69b2/keyrings/cryptfile/convert.py#L132-L142 | [
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"except... | cfa80d4848a5c3c0aeee41a954b2b120c80e69b2 |
test | ArgonAESEncryption._create_cipher | Create the cipher object to encrypt or decrypt a payload. | keyrings/cryptfile/cryptfile.py | def _create_cipher(self, password, salt, nonce = None):
"""
Create the cipher object to encrypt or decrypt a payload.
"""
from argon2.low_level import hash_secret_raw, Type
from Crypto.Cipher import AES
aesmode = self._get_mode(self.aesmode)
if aesmode is None: ... | def _create_cipher(self, password, salt, nonce = None):
"""
Create the cipher object to encrypt or decrypt a payload.
"""
from argon2.low_level import hash_secret_raw, Type
from Crypto.Cipher import AES
aesmode = self._get_mode(self.aesmode)
if aesmode is None: ... | [
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"or",
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] | frispete/keyrings.cryptfile | python | https://github.com/frispete/keyrings.cryptfile/blob/cfa80d4848a5c3c0aeee41a954b2b120c80e69b2/keyrings/cryptfile/cryptfile.py#L38-L58 | [
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"=",
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test | ArgonAESEncryption._get_mode | Return the AES mode, or a list of valid AES modes, if mode == None | keyrings/cryptfile/cryptfile.py | def _get_mode(mode = None):
"""
Return the AES mode, or a list of valid AES modes, if mode == None
"""
from Crypto.Cipher import AES
AESModeMap = {
'CCM': AES.MODE_CCM,
'EAX': AES.MODE_EAX,
'GCM': AES.MODE_GCM,
'OCB': AES.MODE_OCB,... | def _get_mode(mode = None):
"""
Return the AES mode, or a list of valid AES modes, if mode == None
"""
from Crypto.Cipher import AES
AESModeMap = {
'CCM': AES.MODE_CCM,
'EAX': AES.MODE_EAX,
'GCM': AES.MODE_GCM,
'OCB': AES.MODE_OCB,... | [
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"modes",
"if",
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"==",
"None"
] | frispete/keyrings.cryptfile | python | https://github.com/frispete/keyrings.cryptfile/blob/cfa80d4848a5c3c0aeee41a954b2b120c80e69b2/keyrings/cryptfile/cryptfile.py#L61-L76 | [
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":",
"AES",
".",
"MODE_GC... | cfa80d4848a5c3c0aeee41a954b2b120c80e69b2 |
test | CryptFileKeyring.priority | Applicable for all platforms, where the schemes, that are integrated
with your environment, does not fit. | keyrings/cryptfile/cryptfile.py | def priority(self):
"""
Applicable for all platforms, where the schemes, that are integrated
with your environment, does not fit.
"""
try:
__import__('argon2.low_level')
except ImportError: # pragma: no cover
raise RuntimeError("argon2_cffi pac... | def priority(self):
"""
Applicable for all platforms, where the schemes, that are integrated
with your environment, does not fit.
"""
try:
__import__('argon2.low_level')
except ImportError: # pragma: no cover
raise RuntimeError("argon2_cffi pac... | [
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"where",
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"schemes",
"that",
"are",
"integrated",
"with",
"your",
"environment",
"does",
"not",
"fit",
"."
] | frispete/keyrings.cryptfile | python | https://github.com/frispete/keyrings.cryptfile/blob/cfa80d4848a5c3c0aeee41a954b2b120c80e69b2/keyrings/cryptfile/cryptfile.py#L90-L106 | [
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"'Crypto.Cip... | cfa80d4848a5c3c0aeee41a954b2b120c80e69b2 |
test | CryptFileKeyring._check_scheme | check for a valid scheme
raise AttributeError if missing
raise ValueError if not valid | keyrings/cryptfile/cryptfile.py | def _check_scheme(self, config):
"""
check for a valid scheme
raise AttributeError if missing
raise ValueError if not valid
"""
try:
scheme = config.get(
escape_for_ini('keyring-setting'),
escape_for_ini('scheme'),
... | def _check_scheme(self, config):
"""
check for a valid scheme
raise AttributeError if missing
raise ValueError if not valid
"""
try:
scheme = config.get(
escape_for_ini('keyring-setting'),
escape_for_ini('scheme'),
... | [
"check",
"for",
"a",
"valid",
"scheme"
] | frispete/keyrings.cryptfile | python | https://github.com/frispete/keyrings.cryptfile/blob/cfa80d4848a5c3c0aeee41a954b2b120c80e69b2/keyrings/cryptfile/cryptfile.py#L132-L162 | [
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test | startLogging | Starts the global Twisted logger subsystem with maybe
stdout and/or a file specified in the config file | examples/subscriber.py | def startLogging(console=True, filepath=None):
'''
Starts the global Twisted logger subsystem with maybe
stdout and/or a file specified in the config file
'''
global logLevelFilterPredicate
observers = []
if console:
observers.append( FilteringLogObserver(observer=textFileLogObse... | def startLogging(console=True, filepath=None):
'''
Starts the global Twisted logger subsystem with maybe
stdout and/or a file specified in the config file
'''
global logLevelFilterPredicate
observers = []
if console:
observers.append( FilteringLogObserver(observer=textFileLogObse... | [
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"a",
"file",
"specified",
"in",
"the",
"config",
"file"
] | astrorafael/twisted-mqtt | python | https://github.com/astrorafael/twisted-mqtt/blob/5b322f7c2b82a502b1e1b70703ae45f1f668d07d/examples/subscriber.py#L27-L42 | [
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... | 5b322f7c2b82a502b1e1b70703ae45f1f668d07d |
test | setLogLevel | Set a new log level for a given namespace
LevelStr is: 'critical', 'error', 'warn', 'info', 'debug' | examples/subscriber.py | def setLogLevel(namespace=None, levelStr='info'):
'''
Set a new log level for a given namespace
LevelStr is: 'critical', 'error', 'warn', 'info', 'debug'
'''
level = LogLevel.levelWithName(levelStr)
logLevelFilterPredicate.setLogLevelForNamespace(namespace=namespace, level=level) | def setLogLevel(namespace=None, levelStr='info'):
'''
Set a new log level for a given namespace
LevelStr is: 'critical', 'error', 'warn', 'info', 'debug'
'''
level = LogLevel.levelWithName(levelStr)
logLevelFilterPredicate.setLogLevelForNamespace(namespace=namespace, level=level) | [
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] | astrorafael/twisted-mqtt | python | https://github.com/astrorafael/twisted-mqtt/blob/5b322f7c2b82a502b1e1b70703ae45f1f668d07d/examples/subscriber.py#L45-L51 | [
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",... | 5b322f7c2b82a502b1e1b70703ae45f1f668d07d |
test | MQTTService.connectToBroker | Connect to MQTT broker | examples/subscriber.py | def connectToBroker(self, protocol):
'''
Connect to MQTT broker
'''
self.protocol = protocol
self.protocol.onPublish = self.onPublish
self.protocol.onDisconnection = self.onDisconnection
self.protocol.setWindowSize(3)
try:
... | def connectToBroker(self, protocol):
'''
Connect to MQTT broker
'''
self.protocol = protocol
self.protocol.onPublish = self.onPublish
self.protocol.onDisconnection = self.onDisconnection
self.protocol.setWindowSize(3)
try:
... | [
"Connect",
"to",
"MQTT",
"broker"
] | astrorafael/twisted-mqtt | python | https://github.com/astrorafael/twisted-mqtt/blob/5b322f7c2b82a502b1e1b70703ae45f1f668d07d/examples/subscriber.py#L72-L87 | [
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test | MQTTService.onPublish | Callback Receiving messages from publisher | examples/subscriber.py | def onPublish(self, topic, payload, qos, dup, retain, msgId):
'''
Callback Receiving messages from publisher
'''
log.debug("msg={payload}", payload=payload) | def onPublish(self, topic, payload, qos, dup, retain, msgId):
'''
Callback Receiving messages from publisher
'''
log.debug("msg={payload}", payload=payload) | [
"Callback",
"Receiving",
"messages",
"from",
"publisher"
] | astrorafael/twisted-mqtt | python | https://github.com/astrorafael/twisted-mqtt/blob/5b322f7c2b82a502b1e1b70703ae45f1f668d07d/examples/subscriber.py#L117-L121 | [
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"\"msg={payload}\"",
",",
"payload",
"=",
"payload",
")"
] | 5b322f7c2b82a502b1e1b70703ae45f1f668d07d |
test | MQTTService.onDisconnection | get notfied of disconnections
and get a deferred for a new protocol object (next retry) | examples/subscriber.py | def onDisconnection(self, reason):
'''
get notfied of disconnections
and get a deferred for a new protocol object (next retry)
'''
log.debug("<Connection was lost !> <reason={r}>", r=reason)
self.whenConnected().addCallback(self.connectToBroker) | def onDisconnection(self, reason):
'''
get notfied of disconnections
and get a deferred for a new protocol object (next retry)
'''
log.debug("<Connection was lost !> <reason={r}>", r=reason)
self.whenConnected().addCallback(self.connectToBroker) | [
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test | MQTTService.connectToBroker | Connect to MQTT broker | examples/pubsubs.py | def connectToBroker(self, protocol):
'''
Connect to MQTT broker
'''
self.protocol = protocol
self.protocol.onPublish = self.onPublish
self.protocol.onDisconnection = self.onDisconnection
self.protocol.setWindowSize(3)
self.task = task... | def connectToBroker(self, protocol):
'''
Connect to MQTT broker
'''
self.protocol = protocol
self.protocol.onPublish = self.onPublish
self.protocol.onDisconnection = self.onDisconnection
self.protocol.setWindowSize(3)
self.task = task... | [
"Connect",
"to",
"MQTT",
"broker"
] | astrorafael/twisted-mqtt | python | https://github.com/astrorafael/twisted-mqtt/blob/5b322f7c2b82a502b1e1b70703ae45f1f668d07d/examples/pubsubs.py#L72-L89 | [
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test | MQTTFactory.makeId | Produce ids for Protocol packets, outliving their sessions | mqtt/client/factory.py | def makeId(self):
'''Produce ids for Protocol packets, outliving their sessions'''
self.id = (self.id + 1) % 65536
self.id = self.id or 1 # avoid id 0
return self.id | def makeId(self):
'''Produce ids for Protocol packets, outliving their sessions'''
self.id = (self.id + 1) % 65536
self.id = self.id or 1 # avoid id 0
return self.id | [
"Produce",
"ids",
"for",
"Protocol",
"packets",
"outliving",
"their",
"sessions"
] | astrorafael/twisted-mqtt | python | https://github.com/astrorafael/twisted-mqtt/blob/5b322f7c2b82a502b1e1b70703ae45f1f668d07d/mqtt/client/factory.py#L116-L120 | [
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] | 5b322f7c2b82a502b1e1b70703ae45f1f668d07d |
test | BaseState.connect | Send a CONNECT control packet. | mqtt/client/base.py | def connect(self, request):
'''
Send a CONNECT control packet.
'''
state = self.__class__.__name__
return defer.fail(MQTTStateError("Unexpected connect() operation", state)) | def connect(self, request):
'''
Send a CONNECT control packet.
'''
state = self.__class__.__name__
return defer.fail(MQTTStateError("Unexpected connect() operation", state)) | [
"Send",
"a",
"CONNECT",
"control",
"packet",
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] | astrorafael/twisted-mqtt | python | https://github.com/astrorafael/twisted-mqtt/blob/5b322f7c2b82a502b1e1b70703ae45f1f668d07d/mqtt/client/base.py#L100-L105 | [
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test | BaseState.handleCONNACK | Handles CONNACK packet from the server | mqtt/client/base.py | def handleCONNACK(self, response):
'''
Handles CONNACK packet from the server
'''
state = self.__class__.__name__
log.error("Unexpected {packet:7} packet received in {log_source}", packet="CONNACK") | def handleCONNACK(self, response):
'''
Handles CONNACK packet from the server
'''
state = self.__class__.__name__
log.error("Unexpected {packet:7} packet received in {log_source}", packet="CONNACK") | [
"Handles",
"CONNACK",
"packet",
"from",
"the",
"server"
] | astrorafael/twisted-mqtt | python | https://github.com/astrorafael/twisted-mqtt/blob/5b322f7c2b82a502b1e1b70703ae45f1f668d07d/mqtt/client/base.py#L138-L143 | [
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test | IMQTTClientControl.connect | Abstract
========
Send a CONNECT control packet.
Description
===========
After a Network Connection is established by a Client to a Server,
the first Packet sent from the Client to the Server MUST be a CONNECT
Packet [MQTT-3.1.0-1].
A Client can only... | mqtt/client/interfaces.py | def connect(clientId, keepalive=0, willTopic=None,
willMessage=None, willQoS=0, willRetain=False,
username=None, password=None, cleanStart=True, version=mqtt.v311):
'''
Abstract
========
Send a CONNECT control packet.
Description
=======... | def connect(clientId, keepalive=0, willTopic=None,
willMessage=None, willQoS=0, willRetain=False,
username=None, password=None, cleanStart=True, version=mqtt.v311):
'''
Abstract
========
Send a CONNECT control packet.
Description
=======... | [
"Abstract",
"========"
] | astrorafael/twisted-mqtt | python | https://github.com/astrorafael/twisted-mqtt/blob/5b322f7c2b82a502b1e1b70703ae45f1f668d07d/mqtt/client/interfaces.py#L44-L84 | [
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... | 5b322f7c2b82a502b1e1b70703ae45f1f668d07d |
test | encodeString | Encode an UTF-8 string into MQTT format.
Returns a bytearray | mqtt/pdu.py | def encodeString(string):
'''
Encode an UTF-8 string into MQTT format.
Returns a bytearray
'''
encoded = bytearray(2)
encoded.extend(bytearray(string, encoding='utf-8'))
l = len(encoded)-2
if(l > 65535):
raise StringValueError(l)
encoded[0] = l >> 8
encoded[1] = l & 0xFF... | def encodeString(string):
'''
Encode an UTF-8 string into MQTT format.
Returns a bytearray
'''
encoded = bytearray(2)
encoded.extend(bytearray(string, encoding='utf-8'))
l = len(encoded)-2
if(l > 65535):
raise StringValueError(l)
encoded[0] = l >> 8
encoded[1] = l & 0xFF... | [
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] | astrorafael/twisted-mqtt | python | https://github.com/astrorafael/twisted-mqtt/blob/5b322f7c2b82a502b1e1b70703ae45f1f668d07d/mqtt/pdu.py#L51-L63 | [
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... | 5b322f7c2b82a502b1e1b70703ae45f1f668d07d |
test | decodeString | Decodes an UTF-8 string from an encoded MQTT bytearray.
Returns the decoded string and renaining bytearray to be parsed | mqtt/pdu.py | def decodeString(encoded):
'''
Decodes an UTF-8 string from an encoded MQTT bytearray.
Returns the decoded string and renaining bytearray to be parsed
'''
length = encoded[0]*256 + encoded[1]
return (encoded[2:2+length].decode('utf-8'), encoded[2+length:]) | def decodeString(encoded):
'''
Decodes an UTF-8 string from an encoded MQTT bytearray.
Returns the decoded string and renaining bytearray to be parsed
'''
length = encoded[0]*256 + encoded[1]
return (encoded[2:2+length].decode('utf-8'), encoded[2+length:]) | [
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] | astrorafael/twisted-mqtt | python | https://github.com/astrorafael/twisted-mqtt/blob/5b322f7c2b82a502b1e1b70703ae45f1f668d07d/mqtt/pdu.py#L65-L71 | [
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test | encode16Int | Encodes a 16 bit unsigned integer into MQTT format.
Returns a bytearray | mqtt/pdu.py | def encode16Int(value):
'''
Encodes a 16 bit unsigned integer into MQTT format.
Returns a bytearray
'''
value = int(value)
encoded = bytearray(2)
encoded[0] = value >> 8
encoded[1] = value & 0xFF
return encoded | def encode16Int(value):
'''
Encodes a 16 bit unsigned integer into MQTT format.
Returns a bytearray
'''
value = int(value)
encoded = bytearray(2)
encoded[0] = value >> 8
encoded[1] = value & 0xFF
return encoded | [
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] | astrorafael/twisted-mqtt | python | https://github.com/astrorafael/twisted-mqtt/blob/5b322f7c2b82a502b1e1b70703ae45f1f668d07d/mqtt/pdu.py#L74-L83 | [
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test | encodeLength | Encodes value into a multibyte sequence defined by MQTT protocol.
Used to encode packet length fields. | mqtt/pdu.py | def encodeLength(value):
'''
Encodes value into a multibyte sequence defined by MQTT protocol.
Used to encode packet length fields.
'''
encoded = bytearray()
while True:
digit = value % 128
value //= 128
if value > 0:
digit |= 128
encoded.append(digit)... | def encodeLength(value):
'''
Encodes value into a multibyte sequence defined by MQTT protocol.
Used to encode packet length fields.
'''
encoded = bytearray()
while True:
digit = value % 128
value //= 128
if value > 0:
digit |= 128
encoded.append(digit)... | [
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] | astrorafael/twisted-mqtt | python | https://github.com/astrorafael/twisted-mqtt/blob/5b322f7c2b82a502b1e1b70703ae45f1f668d07d/mqtt/pdu.py#L92-L106 | [
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... | 5b322f7c2b82a502b1e1b70703ae45f1f668d07d |
test | decodeLength | Decodes a variable length value defined in the MQTT protocol.
This value typically represents remaining field lengths | mqtt/pdu.py | def decodeLength(encoded):
'''
Decodes a variable length value defined in the MQTT protocol.
This value typically represents remaining field lengths
'''
value = 0
multiplier = 1
for i in encoded:
value += (i & 0x7F) * multiplier
multiplier *= 0x80
if (i & 0x80) !... | def decodeLength(encoded):
'''
Decodes a variable length value defined in the MQTT protocol.
This value typically represents remaining field lengths
'''
value = 0
multiplier = 1
for i in encoded:
value += (i & 0x7F) * multiplier
multiplier *= 0x80
if (i & 0x80) !... | [
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] | astrorafael/twisted-mqtt | python | https://github.com/astrorafael/twisted-mqtt/blob/5b322f7c2b82a502b1e1b70703ae45f1f668d07d/mqtt/pdu.py#L109-L121 | [
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")"... | 5b322f7c2b82a502b1e1b70703ae45f1f668d07d |
test | DISCONNECT.encode | Encode and store a DISCONNECT control packet. | mqtt/pdu.py | def encode(self):
'''
Encode and store a DISCONNECT control packet.
'''
header = bytearray(2)
header[0] = 0xE0
self.encoded = header
return str(header) if PY2 else bytes(header) | def encode(self):
'''
Encode and store a DISCONNECT control packet.
'''
header = bytearray(2)
header[0] = 0xE0
self.encoded = header
return str(header) if PY2 else bytes(header) | [
"Encode",
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"a",
"DISCONNECT",
"control",
"packet",
"."
] | astrorafael/twisted-mqtt | python | https://github.com/astrorafael/twisted-mqtt/blob/5b322f7c2b82a502b1e1b70703ae45f1f668d07d/mqtt/pdu.py#L133-L140 | [
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] | 5b322f7c2b82a502b1e1b70703ae45f1f668d07d |
test | CONNECT.encode | Encode and store a CONNECT control packet.
@raise e: C{ValueError} if any encoded topic string exceeds 65535 bytes.
@raise e: C{ValueError} if encoded username string exceeds 65535 bytes. | mqtt/pdu.py | def encode(self):
'''
Encode and store a CONNECT control packet.
@raise e: C{ValueError} if any encoded topic string exceeds 65535 bytes.
@raise e: C{ValueError} if encoded username string exceeds 65535 bytes.
'''
header = bytearray(1)
varHeader = bytearray()
... | def encode(self):
'''
Encode and store a CONNECT control packet.
@raise e: C{ValueError} if any encoded topic string exceeds 65535 bytes.
@raise e: C{ValueError} if encoded username string exceeds 65535 bytes.
'''
header = bytearray(1)
varHeader = bytearray()
... | [
"Encode",
"and",
"store",
"a",
"CONNECT",
"control",
"packet",
"."
] | astrorafael/twisted-mqtt | python | https://github.com/astrorafael/twisted-mqtt/blob/5b322f7c2b82a502b1e1b70703ae45f1f668d07d/mqtt/pdu.py#L211-L249 | [
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"# ---- Variable header encoding section... | 5b322f7c2b82a502b1e1b70703ae45f1f668d07d |
test | CONNECT.decode | Decode a CONNECT control packet. | mqtt/pdu.py | def decode(self, packet):
'''
Decode a CONNECT control packet.
'''
self.encoded = packet
# Strip the fixed header plus variable length field
lenLen = 1
while packet[lenLen] & 0x80:
lenLen += 1
packet_remaining = packet[lenLen+1:]
# Var... | def decode(self, packet):
'''
Decode a CONNECT control packet.
'''
self.encoded = packet
# Strip the fixed header plus variable length field
lenLen = 1
while packet[lenLen] & 0x80:
lenLen += 1
packet_remaining = packet[lenLen+1:]
# Var... | [
"Decode",
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"."
] | astrorafael/twisted-mqtt | python | https://github.com/astrorafael/twisted-mqtt/blob/5b322f7c2b82a502b1e1b70703ae45f1f668d07d/mqtt/pdu.py#L251-L289 | [
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test | CONNACK.encode | Encode and store a CONNACK control packet. | mqtt/pdu.py | def encode(self):
'''
Encode and store a CONNACK control packet.
'''
header = bytearray(1)
varHeader = bytearray(2)
header[0] = 0x20
varHeader[0] = self.session
varHeader[1] = self.resultCode
header.extend(encodeLength(len(varHe... | def encode(self):
'''
Encode and store a CONNACK control packet.
'''
header = bytearray(1)
varHeader = bytearray(2)
header[0] = 0x20
varHeader[0] = self.session
varHeader[1] = self.resultCode
header.extend(encodeLength(len(varHe... | [
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"control",
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"."
] | astrorafael/twisted-mqtt | python | https://github.com/astrorafael/twisted-mqtt/blob/5b322f7c2b82a502b1e1b70703ae45f1f668d07d/mqtt/pdu.py#L302-L315 | [
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... | 5b322f7c2b82a502b1e1b70703ae45f1f668d07d |
test | CONNACK.decode | Decode a CONNACK control packet. | mqtt/pdu.py | def decode(self, packet):
'''
Decode a CONNACK control packet.
'''
self.encoded = packet
# Strip the fixed header plus variable length field
lenLen = 1
while packet[lenLen] & 0x80:
lenLen += 1
packet_remaining = packet[lenLen+1:]
self.... | def decode(self, packet):
'''
Decode a CONNACK control packet.
'''
self.encoded = packet
# Strip the fixed header plus variable length field
lenLen = 1
while packet[lenLen] & 0x80:
lenLen += 1
packet_remaining = packet[lenLen+1:]
self.... | [
"Decode",
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] | astrorafael/twisted-mqtt | python | https://github.com/astrorafael/twisted-mqtt/blob/5b322f7c2b82a502b1e1b70703ae45f1f668d07d/mqtt/pdu.py#L317-L328 | [
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test | SUBSCRIBE.decode | Decode a SUBSCRIBE control packet. | mqtt/pdu.py | def decode(self, packet):
'''
Decode a SUBSCRIBE control packet.
'''
self.encoded = packet
lenLen = 1
while packet[lenLen] & 0x80:
lenLen += 1
packet_remaining = packet[lenLen+1:]
self.msgId = decode16Int(packet_remaining[0:2])
self.... | def decode(self, packet):
'''
Decode a SUBSCRIBE control packet.
'''
self.encoded = packet
lenLen = 1
while packet[lenLen] & 0x80:
lenLen += 1
packet_remaining = packet[lenLen+1:]
self.msgId = decode16Int(packet_remaining[0:2])
self.... | [
"Decode",
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"control",
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"."
] | astrorafael/twisted-mqtt | python | https://github.com/astrorafael/twisted-mqtt/blob/5b322f7c2b82a502b1e1b70703ae45f1f668d07d/mqtt/pdu.py#L357-L373 | [
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"1"... | 5b322f7c2b82a502b1e1b70703ae45f1f668d07d |
test | SUBACK.encode | Encode and store a SUBACK control packet. | mqtt/pdu.py | def encode(self):
'''
Encode and store a SUBACK control packet.
'''
header = bytearray(1)
payload = bytearray()
varHeader = encode16Int(self.msgId)
header[0] = 0x90
for code in self.granted:
payload.append(code[0] | (0x80 if code[1] == Tru... | def encode(self):
'''
Encode and store a SUBACK control packet.
'''
header = bytearray(1)
payload = bytearray()
varHeader = encode16Int(self.msgId)
header[0] = 0x90
for code in self.granted:
payload.append(code[0] | (0x80 if code[1] == Tru... | [
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"a",
"SUBACK",
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"."
] | astrorafael/twisted-mqtt | python | https://github.com/astrorafael/twisted-mqtt/blob/5b322f7c2b82a502b1e1b70703ae45f1f668d07d/mqtt/pdu.py#L387-L401 | [
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test | UNSUBSCRIBE.encode | Encode and store an UNSUBCRIBE control packet
@raise e: C{ValueError} if any encoded topic string exceeds 65535 bytes | mqtt/pdu.py | def encode(self):
'''
Encode and store an UNSUBCRIBE control packet
@raise e: C{ValueError} if any encoded topic string exceeds 65535 bytes
'''
header = bytearray(1)
payload = bytearray()
varHeader = encode16Int(self.msgId)
header[0] = 0xA2 # packe... | def encode(self):
'''
Encode and store an UNSUBCRIBE control packet
@raise e: C{ValueError} if any encoded topic string exceeds 65535 bytes
'''
header = bytearray(1)
payload = bytearray()
varHeader = encode16Int(self.msgId)
header[0] = 0xA2 # packe... | [
"Encode",
"and",
"store",
"an",
"UNSUBCRIBE",
"control",
"packet"
] | astrorafael/twisted-mqtt | python | https://github.com/astrorafael/twisted-mqtt/blob/5b322f7c2b82a502b1e1b70703ae45f1f668d07d/mqtt/pdu.py#L430-L445 | [
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"for... | 5b322f7c2b82a502b1e1b70703ae45f1f668d07d |
test | UNSUBSCRIBE.decode | Decode a UNSUBACK control packet. | mqtt/pdu.py | def decode(self, packet):
'''
Decode a UNSUBACK control packet.
'''
self.encoded = packet
lenLen = 1
while packet[lenLen] & 0x80:
lenLen += 1
packet_remaining = packet[lenLen+1:]
self.msgId = decode16Int(packet_remaining[0:2])
self.t... | def decode(self, packet):
'''
Decode a UNSUBACK control packet.
'''
self.encoded = packet
lenLen = 1
while packet[lenLen] & 0x80:
lenLen += 1
packet_remaining = packet[lenLen+1:]
self.msgId = decode16Int(packet_remaining[0:2])
self.t... | [
"Decode",
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"UNSUBACK",
"control",
"packet",
"."
] | astrorafael/twisted-mqtt | python | https://github.com/astrorafael/twisted-mqtt/blob/5b322f7c2b82a502b1e1b70703ae45f1f668d07d/mqtt/pdu.py#L447-L463 | [
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test | UNSUBACK.encode | Encode and store an UNSUBACK control packet | mqtt/pdu.py | def encode(self):
'''
Encode and store an UNSUBACK control packet
'''
header = bytearray(1)
varHeader = encode16Int(self.msgId)
header[0] = 0xB0
header.extend(encodeLength(len(varHeader)))
header.extend(varHeader)
self.encoded = header
... | def encode(self):
'''
Encode and store an UNSUBACK control packet
'''
header = bytearray(1)
varHeader = encode16Int(self.msgId)
header[0] = 0xB0
header.extend(encodeLength(len(varHeader)))
header.extend(varHeader)
self.encoded = header
... | [
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"control",
"packet"
] | astrorafael/twisted-mqtt | python | https://github.com/astrorafael/twisted-mqtt/blob/5b322f7c2b82a502b1e1b70703ae45f1f668d07d/mqtt/pdu.py#L474-L484 | [
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... | 5b322f7c2b82a502b1e1b70703ae45f1f668d07d |
test | PUBLISH.encode | Encode and store a PUBLISH control packet.
@raise e: C{ValueError} if encoded topic string exceeds 65535 bytes.
@raise e: C{ValueError} if encoded packet size exceeds 268435455 bytes.
@raise e: C{TypeError} if C{data} is not a string, bytearray, int, boolean or float. | mqtt/pdu.py | def encode(self):
'''
Encode and store a PUBLISH control packet.
@raise e: C{ValueError} if encoded topic string exceeds 65535 bytes.
@raise e: C{ValueError} if encoded packet size exceeds 268435455 bytes.
@raise e: C{TypeError} if C{data} is not a string, bytearray, int, boolean... | def encode(self):
'''
Encode and store a PUBLISH control packet.
@raise e: C{ValueError} if encoded topic string exceeds 65535 bytes.
@raise e: C{ValueError} if encoded packet size exceeds 268435455 bytes.
@raise e: C{TypeError} if C{data} is not a string, bytearray, int, boolean... | [
"Encode",
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"PUBLISH",
"control",
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"."
] | astrorafael/twisted-mqtt | python | https://github.com/astrorafael/twisted-mqtt/blob/5b322f7c2b82a502b1e1b70703ae45f1f668d07d/mqtt/pdu.py#L511-L542 | [
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"... | 5b322f7c2b82a502b1e1b70703ae45f1f668d07d |
test | PUBLISH.decode | Decode a PUBLISH control packet. | mqtt/pdu.py | def decode(self, packet):
'''
Decode a PUBLISH control packet.
'''
self.encoded = packet
lenLen = 1
while packet[lenLen] & 0x80:
lenLen += 1
packet_remaining = packet[lenLen+1:]
self.dup = (packet[0] & 0x08) == 0x08
self.qos = (p... | def decode(self, packet):
'''
Decode a PUBLISH control packet.
'''
self.encoded = packet
lenLen = 1
while packet[lenLen] & 0x80:
lenLen += 1
packet_remaining = packet[lenLen+1:]
self.dup = (packet[0] & 0x08) == 0x08
self.qos = (p... | [
"Decode",
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"PUBLISH",
"control",
"packet",
"."
] | astrorafael/twisted-mqtt | python | https://github.com/astrorafael/twisted-mqtt/blob/5b322f7c2b82a502b1e1b70703ae45f1f668d07d/mqtt/pdu.py#L544-L563 | [
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"1"... | 5b322f7c2b82a502b1e1b70703ae45f1f668d07d |
test | PUBREL.decode | Decode a PUBREL control packet. | mqtt/pdu.py | def decode(self, packet):
'''
Decode a PUBREL control packet.
'''
self.encoded = packet
lenLen = 1
while packet[lenLen] & 0x80:
lenLen += 1
packet_remaining = packet[lenLen+1:]
self.msgId = decode16Int(packet_remaining)
self.dup = (pa... | def decode(self, packet):
'''
Decode a PUBREL control packet.
'''
self.encoded = packet
lenLen = 1
while packet[lenLen] & 0x80:
lenLen += 1
packet_remaining = packet[lenLen+1:]
self.msgId = decode16Int(packet_remaining)
self.dup = (pa... | [
"Decode",
"a",
"PUBREL",
"control",
"packet",
"."
] | astrorafael/twisted-mqtt | python | https://github.com/astrorafael/twisted-mqtt/blob/5b322f7c2b82a502b1e1b70703ae45f1f668d07d/mqtt/pdu.py#L651-L661 | [
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test | API.get_url | Return url for call method.
:param method (optional): `str` method name.
:returns: `str` URL. | vklancer/api.py | def get_url(self, method=None, **kwargs):
"""Return url for call method.
:param method (optional): `str` method name.
:returns: `str` URL.
"""
kwargs.setdefault('v', self.__version)
if self.__token is not None:
kwargs.setdefault('access_token', self.__token)... | def get_url(self, method=None, **kwargs):
"""Return url for call method.
:param method (optional): `str` method name.
:returns: `str` URL.
"""
kwargs.setdefault('v', self.__version)
if self.__token is not None:
kwargs.setdefault('access_token', self.__token)... | [
"Return",
"url",
"for",
"call",
"method",
"."
] | bindlock/vklancer | python | https://github.com/bindlock/vklancer/blob/10151c3856bc6f46a1f446ae4d605d46aace3669/vklancer/api.py#L26-L39 | [
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"setde... | 10151c3856bc6f46a1f446ae4d605d46aace3669 |
test | API.request | Send request to API.
:param method: `str` method name.
:returns: `dict` response. | vklancer/api.py | def request(self, method, **kwargs):
"""
Send request to API.
:param method: `str` method name.
:returns: `dict` response.
"""
kwargs.setdefault('v', self.__version)
if self.__token is not None:
kwargs.setdefault('access_token', self.__token)
... | def request(self, method, **kwargs):
"""
Send request to API.
:param method: `str` method name.
:returns: `dict` response.
"""
kwargs.setdefault('v', self.__version)
if self.__token is not None:
kwargs.setdefault('access_token', self.__token)
... | [
"Send",
"request",
"to",
"API",
"."
] | bindlock/vklancer | python | https://github.com/bindlock/vklancer/blob/10151c3856bc6f46a1f446ae4d605d46aace3669/vklancer/api.py#L41-L53 | [
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... | 10151c3856bc6f46a1f446ae4d605d46aace3669 |
test | authentication | Authentication on vk.com.
:param login: login on vk.com.
:param password: password on vk.com.
:returns: `requests.Session` session with cookies. | vklancer/utils.py | def authentication(login, password):
"""
Authentication on vk.com.
:param login: login on vk.com.
:param password: password on vk.com.
:returns: `requests.Session` session with cookies.
"""
session = requests.Session()
response = session.get('https://m.vk.com')
url = re.search(r'act... | def authentication(login, password):
"""
Authentication on vk.com.
:param login: login on vk.com.
:param password: password on vk.com.
:returns: `requests.Session` session with cookies.
"""
session = requests.Session()
response = session.get('https://m.vk.com')
url = re.search(r'act... | [
"Authentication",
"on",
"vk",
".",
"com",
"."
] | bindlock/vklancer | python | https://github.com/bindlock/vklancer/blob/10151c3856bc6f46a1f446ae4d605d46aace3669/vklancer/utils.py#L8-L21 | [
"def",
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"search",
"(",
"r'action=\"([^\\\"]+)\"'",
... | 10151c3856bc6f46a1f446ae4d605d46aace3669 |
test | oauth | OAuth on vk.com.
:param login: login on vk.com.
:param password: password on vk.com.
:param app_id: vk.com application id (default: 4729418).
:param scope: allowed actions (default: 2097151 (all)).
:returns: OAuth2 access token or None. | vklancer/utils.py | def oauth(login, password, app_id=4729418, scope=2097151):
"""
OAuth on vk.com.
:param login: login on vk.com.
:param password: password on vk.com.
:param app_id: vk.com application id (default: 4729418).
:param scope: allowed actions (default: 2097151 (all)).
:returns: OAuth2 access token ... | def oauth(login, password, app_id=4729418, scope=2097151):
"""
OAuth on vk.com.
:param login: login on vk.com.
:param password: password on vk.com.
:param app_id: vk.com application id (default: 4729418).
:param scope: allowed actions (default: 2097151 (all)).
:returns: OAuth2 access token ... | [
"OAuth",
"on",
"vk",
".",
"com",
"."
] | bindlock/vklancer | python | https://github.com/bindlock/vklancer/blob/10151c3856bc6f46a1f446ae4d605d46aace3669/vklancer/utils.py#L24-L50 | [
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"=",
"{",
"'response_type'",
":",
"'token'",
",",
"'client... | 10151c3856bc6f46a1f446ae4d605d46aace3669 |
test | File.create_from_array | create a block from array like objects
The operation is well defined only if array is at most 2d.
Parameters
----------
array : array_like,
array shall have a scalar dtype.
blockname : string
name of the block
Nfil... | bigfile/__init__.py | def create_from_array(self, blockname, array, Nfile=None, memorylimit=1024 * 1024 * 256):
""" create a block from array like objects
The operation is well defined only if array is at most 2d.
Parameters
----------
array : array_like,
array shall h... | def create_from_array(self, blockname, array, Nfile=None, memorylimit=1024 * 1024 * 256):
""" create a block from array like objects
The operation is well defined only if array is at most 2d.
Parameters
----------
array : array_like,
array shall h... | [
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"operation",
"is",
"well",
"defined",
"only",
"if",
"array",
"is",
"at",
"most",
"2d",
"."
] | rainwoodman/bigfile | python | https://github.com/rainwoodman/bigfile/blob/1a2d05977fc8edebd8ddf9e81fdb97648596266d/bigfile/__init__.py#L96-L135 | [
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"(",
"array",
")",
"# sane value -- 32 million items per physical file",... | 1a2d05977fc8edebd8ddf9e81fdb97648596266d |
test | FileMPI.refresh | Refresh the list of blocks to the disk, collectively | bigfile/__init__.py | def refresh(self):
""" Refresh the list of blocks to the disk, collectively """
if self.comm.rank == 0:
self._blocks = self.list_blocks()
else:
self._blocks = None
self._blocks = self.comm.bcast(self._blocks) | def refresh(self):
""" Refresh the list of blocks to the disk, collectively """
if self.comm.rank == 0:
self._blocks = self.list_blocks()
else:
self._blocks = None
self._blocks = self.comm.bcast(self._blocks) | [
"Refresh",
"the",
"list",
"of",
"blocks",
"to",
"the",
"disk",
"collectively"
] | rainwoodman/bigfile | python | https://github.com/rainwoodman/bigfile/blob/1a2d05977fc8edebd8ddf9e81fdb97648596266d/bigfile/__init__.py#L199-L205 | [
"def",
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"=",
"None",
"self",
".",
"_blocks",
"=",
"se... | 1a2d05977fc8edebd8ddf9e81fdb97648596266d |
test | FileMPI.create_from_array | create a block from array like objects
The operation is well defined only if array is at most 2d.
Parameters
----------
array : array_like,
array shall have a scalar dtype.
blockname : string
name of the block
Nfil... | bigfile/__init__.py | def create_from_array(self, blockname, array, Nfile=None, memorylimit=1024 * 1024 * 256):
""" create a block from array like objects
The operation is well defined only if array is at most 2d.
Parameters
----------
array : array_like,
array shall h... | def create_from_array(self, blockname, array, Nfile=None, memorylimit=1024 * 1024 * 256):
""" create a block from array like objects
The operation is well defined only if array is at most 2d.
Parameters
----------
array : array_like,
array shall h... | [
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"only",
"if",
"array",
"is",
"at",
"most",
"2d",
"."
] | rainwoodman/bigfile | python | https://github.com/rainwoodman/bigfile/blob/1a2d05977fc8edebd8ddf9e81fdb97648596266d/bigfile/__init__.py#L221-L261 | [
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"allreduce",
"(",
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"(",
"array",
")",... | 1a2d05977fc8edebd8ddf9e81fdb97648596266d |
test | maybebool | If `value` is a string type, attempts to convert it to a boolean
if it looks like it might be one, otherwise returns the value
unchanged. The difference between this and
:func:`pyramid.settings.asbool` is how non-bools are handled: this
returns the original value, whereas `asbool` returns False. | pyramid_webassets/__init__.py | def maybebool(value):
'''
If `value` is a string type, attempts to convert it to a boolean
if it looks like it might be one, otherwise returns the value
unchanged. The difference between this and
:func:`pyramid.settings.asbool` is how non-bools are handled: this
returns the original value, where... | def maybebool(value):
'''
If `value` is a string type, attempts to convert it to a boolean
if it looks like it might be one, otherwise returns the value
unchanged. The difference between this and
:func:`pyramid.settings.asbool` is how non-bools are handled: this
returns the original value, where... | [
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"it",
"to",
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"looks",
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"be",
"one",
"otherwise",
"returns",
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"value",
"unchanged",
".",
"The",
"difference",
"between",
"this",
... | sontek/pyramid_webassets | python | https://github.com/sontek/pyramid_webassets/blob/d81a8f0c55aa49181ced4650fc88d434bbf94e62/pyramid_webassets/__init__.py#L24-L34 | [
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")",
"# pragma: no cover",
"return",
"value"... | d81a8f0c55aa49181ced4650fc88d434bbf94e62 |
test | get_webassets_env_from_settings | This function will take all webassets.* parameters, and
call the ``Environment()`` constructor with kwargs passed in.
The only two parameters that are not passed as keywords are:
* base_dir
* base_url
which are passed in positionally.
Read the ``WebAssets`` docs for ``Environment`` for more ... | pyramid_webassets/__init__.py | def get_webassets_env_from_settings(settings, prefix='webassets'):
"""This function will take all webassets.* parameters, and
call the ``Environment()`` constructor with kwargs passed in.
The only two parameters that are not passed as keywords are:
* base_dir
* base_url
which are passed in po... | def get_webassets_env_from_settings(settings, prefix='webassets'):
"""This function will take all webassets.* parameters, and
call the ``Environment()`` constructor with kwargs passed in.
The only two parameters that are not passed as keywords are:
* base_dir
* base_url
which are passed in po... | [
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"parameters",
"and",
"call",
"the",
"Environment",
"()",
"constructor",
"with",
"kwargs",
"passed",
"in",
"."
] | sontek/pyramid_webassets | python | https://github.com/sontek/pyramid_webassets/blob/d81a8f0c55aa49181ced4650fc88d434bbf94e62/pyramid_webassets/__init__.py#L207-L328 | [
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"cut_prefix",
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"+",
"1",
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... | d81a8f0c55aa49181ced4650fc88d434bbf94e62 |
test | classifier.format_data | Function for converting a dict to an array suitable for sklearn.
Parameters
----------
data : dict
A dict of data, containing all elements of
`analytes` as items.
scale : bool
Whether or not to scale the data. Should always be
`True`, unle... | latools/filtering/classifier_obj.py | def format_data(self, data, scale=True):
"""
Function for converting a dict to an array suitable for sklearn.
Parameters
----------
data : dict
A dict of data, containing all elements of
`analytes` as items.
scale : bool
Whether or not... | def format_data(self, data, scale=True):
"""
Function for converting a dict to an array suitable for sklearn.
Parameters
----------
data : dict
A dict of data, containing all elements of
`analytes` as items.
scale : bool
Whether or not... | [
"Function",
"for",
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"a",
"dict",
"to",
"an",
"array",
"suitable",
"for",
"sklearn",
"."
] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/filtering/classifier_obj.py#L28-L65 | [
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"[",
"0... | cd25a650cfee318152f234d992708511f7047fbe |
test | classifier.fitting_data | Function to format data for cluster fitting.
Parameters
----------
data : dict
A dict of data, containing all elements of
`analytes` as items.
Returns
-------
A data array for initial cluster fitting. | latools/filtering/classifier_obj.py | def fitting_data(self, data):
"""
Function to format data for cluster fitting.
Parameters
----------
data : dict
A dict of data, containing all elements of
`analytes` as items.
Returns
-------
A data array for initial cluster fitt... | def fitting_data(self, data):
"""
Function to format data for cluster fitting.
Parameters
----------
data : dict
A dict of data, containing all elements of
`analytes` as items.
Returns
-------
A data array for initial cluster fitt... | [
"Function",
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"for",
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"fitting",
"."
] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/filtering/classifier_obj.py#L67-L87 | [
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"(",
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test | classifier.fit_kmeans | Fit KMeans clustering algorithm to data.
Parameters
----------
data : array-like
A dataset formatted by `classifier.fitting_data`.
n_clusters : int
The number of clusters in the data.
**kwargs
passed to `sklearn.cluster.KMeans`.
Retur... | latools/filtering/classifier_obj.py | def fit_kmeans(self, data, n_clusters, **kwargs):
"""
Fit KMeans clustering algorithm to data.
Parameters
----------
data : array-like
A dataset formatted by `classifier.fitting_data`.
n_clusters : int
The number of clusters in the data.
*... | def fit_kmeans(self, data, n_clusters, **kwargs):
"""
Fit KMeans clustering algorithm to data.
Parameters
----------
data : array-like
A dataset formatted by `classifier.fitting_data`.
n_clusters : int
The number of clusters in the data.
*... | [
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] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/filtering/classifier_obj.py#L89-L108 | [
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test | classifier.fit_meanshift | Fit MeanShift clustering algorithm to data.
Parameters
----------
data : array-like
A dataset formatted by `classifier.fitting_data`.
bandwidth : float
The bandwidth value used during clustering.
If none, determined automatically. Note:
th... | latools/filtering/classifier_obj.py | def fit_meanshift(self, data, bandwidth=None, bin_seeding=False, **kwargs):
"""
Fit MeanShift clustering algorithm to data.
Parameters
----------
data : array-like
A dataset formatted by `classifier.fitting_data`.
bandwidth : float
The bandwidth v... | def fit_meanshift(self, data, bandwidth=None, bin_seeding=False, **kwargs):
"""
Fit MeanShift clustering algorithm to data.
Parameters
----------
data : array-like
A dataset formatted by `classifier.fitting_data`.
bandwidth : float
The bandwidth v... | [
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] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/filtering/classifier_obj.py#L110-L137 | [
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test | classifier.fit | fit classifiers from large dataset.
Parameters
----------
data : dict
A dict of data for clustering. Must contain
items with the same name as analytes used for
clustering.
method : str
A string defining the clustering method used. Can be:
... | latools/filtering/classifier_obj.py | def fit(self, data, method='kmeans', **kwargs):
"""
fit classifiers from large dataset.
Parameters
----------
data : dict
A dict of data for clustering. Must contain
items with the same name as analytes used for
clustering.
method : st... | def fit(self, data, method='kmeans', **kwargs):
"""
fit classifiers from large dataset.
Parameters
----------
data : dict
A dict of data for clustering. Must contain
items with the same name as analytes used for
clustering.
method : st... | [
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] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/filtering/classifier_obj.py#L139-L190 | [
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test | classifier.predict | Label new data with cluster identities.
Parameters
----------
data : dict
A data dict containing the same analytes used to
fit the classifier.
sort_by : str
The name of an analyte used to sort the resulting
clusters. If None, defaults to t... | latools/filtering/classifier_obj.py | def predict(self, data):
"""
Label new data with cluster identities.
Parameters
----------
data : dict
A data dict containing the same analytes used to
fit the classifier.
sort_by : str
The name of an analyte used to sort the resulting... | def predict(self, data):
"""
Label new data with cluster identities.
Parameters
----------
data : dict
A data dict containing the same analytes used to
fit the classifier.
sort_by : str
The name of an analyte used to sort the resulting... | [
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] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/filtering/classifier_obj.py#L192-L218 | [
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test | classifier.map_clusters | Translate cluster identity back to original data size.
Parameters
----------
size : int
size of original dataset
sampled : array-like
integer array describing location of finite values
in original data.
clusters : array-like
intege... | latools/filtering/classifier_obj.py | def map_clusters(self, size, sampled, clusters):
"""
Translate cluster identity back to original data size.
Parameters
----------
size : int
size of original dataset
sampled : array-like
integer array describing location of finite values
... | def map_clusters(self, size, sampled, clusters):
"""
Translate cluster identity back to original data size.
Parameters
----------
size : int
size of original dataset
sampled : array-like
integer array describing location of finite values
... | [
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test | classifier.sort_clusters | Sort clusters by the concentration of a particular analyte.
Parameters
----------
data : dict
A dataset containing sort_by as a key.
cs : array-like
An array of clusters, the same length as values of data.
sort_by : str
analyte to sort the clu... | latools/filtering/classifier_obj.py | def sort_clusters(self, data, cs, sort_by):
"""
Sort clusters by the concentration of a particular analyte.
Parameters
----------
data : dict
A dataset containing sort_by as a key.
cs : array-like
An array of clusters, the same length as values of... | def sort_clusters(self, data, cs, sort_by):
"""
Sort clusters by the concentration of a particular analyte.
Parameters
----------
data : dict
A dataset containing sort_by as a key.
cs : array-like
An array of clusters, the same length as values of... | [
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] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/filtering/classifier_obj.py#L247-L281 | [
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test | get_date | Return a datetime oject from a string, with optional time format.
Parameters
----------
datetime : str
Date-time as string in any sensible format.
time_format : datetime str (optional)
String describing the datetime format. If missing uses
dateutil.parser to guess time format. | latools/helpers/helpers.py | def get_date(datetime, time_format=None):
"""
Return a datetime oject from a string, with optional time format.
Parameters
----------
datetime : str
Date-time as string in any sensible format.
time_format : datetime str (optional)
String describing the datetime format. If missin... | def get_date(datetime, time_format=None):
"""
Return a datetime oject from a string, with optional time format.
Parameters
----------
datetime : str
Date-time as string in any sensible format.
time_format : datetime str (optional)
String describing the datetime format. If missin... | [
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] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/helpers/helpers.py#L29-L45 | [
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... | cd25a650cfee318152f234d992708511f7047fbe |
test | get_total_n_points | Returns the total number of data points in values of dict.
Paramters
---------
d : dict | latools/helpers/helpers.py | def get_total_n_points(d):
"""
Returns the total number of data points in values of dict.
Paramters
---------
d : dict
"""
n = 0
for di in d.values():
n += len(di)
return n | def get_total_n_points(d):
"""
Returns the total number of data points in values of dict.
Paramters
---------
d : dict
"""
n = 0
for di in d.values():
n += len(di)
return n | [
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] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/helpers/helpers.py#L47-L58 | [
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] | cd25a650cfee318152f234d992708511f7047fbe |
test | get_total_time_span | Returns total length of analysis. | latools/helpers/helpers.py | def get_total_time_span(d):
"""
Returns total length of analysis.
"""
tmax = 0
for di in d.values():
if di.uTime.max() > tmax:
tmax = di.uTime.max()
return tmax | def get_total_time_span(d):
"""
Returns total length of analysis.
"""
tmax = 0
for di in d.values():
if di.uTime.max() > tmax:
tmax = di.uTime.max()
return tmax | [
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test | unitpicker | Determines the most appropriate plotting unit for data.
Parameters
----------
a : float or array-like
number to optimise. If array like, the 25% quantile is optimised.
llim : float
minimum allowable value in scaled data.
Returns
-------
(float, str)
(multiplier, uni... | latools/helpers/helpers.py | def unitpicker(a, llim=0.1, denominator=None, focus_stage=None):
"""
Determines the most appropriate plotting unit for data.
Parameters
----------
a : float or array-like
number to optimise. If array like, the 25% quantile is optimised.
llim : float
minimum allowable value in sc... | def unitpicker(a, llim=0.1, denominator=None, focus_stage=None):
"""
Determines the most appropriate plotting unit for data.
Parameters
----------
a : float or array-like
number to optimise. If array like, the 25% quantile is optimised.
llim : float
minimum allowable value in sc... | [
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test | pretty_element | Returns formatted element name.
Parameters
----------
s : str
of format [A-Z][a-z]?[0-9]+
Returns
-------
str
LaTeX formatted string with superscript numbers. | latools/helpers/helpers.py | def pretty_element(s):
"""
Returns formatted element name.
Parameters
----------
s : str
of format [A-Z][a-z]?[0-9]+
Returns
-------
str
LaTeX formatted string with superscript numbers.
"""
el = re.match('.*?([A-z]{1,3}).*?', s).groups()[0]
m = re.match('.*?... | def pretty_element(s):
"""
Returns formatted element name.
Parameters
----------
s : str
of format [A-Z][a-z]?[0-9]+
Returns
-------
str
LaTeX formatted string with superscript numbers.
"""
el = re.match('.*?([A-z]{1,3}).*?', s).groups()[0]
m = re.match('.*?... | [
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] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/helpers/helpers.py#L130-L147 | [
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test | analyte_2_namemass | Converts analytes in format '27Al' to 'Al27'.
Parameters
----------
s : str
of format [A-z]{1,3}[0-9]{1,3}
Returns
-------
str
Name in format [0-9]{1,3}[A-z]{1,3} | latools/helpers/helpers.py | def analyte_2_namemass(s):
"""
Converts analytes in format '27Al' to 'Al27'.
Parameters
----------
s : str
of format [A-z]{1,3}[0-9]{1,3}
Returns
-------
str
Name in format [0-9]{1,3}[A-z]{1,3}
"""
el = re.match('.*?([A-z]{1,3}).*?', s).groups()[0]
m = re.ma... | def analyte_2_namemass(s):
"""
Converts analytes in format '27Al' to 'Al27'.
Parameters
----------
s : str
of format [A-z]{1,3}[0-9]{1,3}
Returns
-------
str
Name in format [0-9]{1,3}[A-z]{1,3}
"""
el = re.match('.*?([A-z]{1,3}).*?', s).groups()[0]
m = re.ma... | [
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] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/helpers/helpers.py#L149-L166 | [
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test | analyte_2_massname | Converts analytes in format 'Al27' to '27Al'.
Parameters
----------
s : str
of format [0-9]{1,3}[A-z]{1,3}
Returns
-------
str
Name in format [A-z]{1,3}[0-9]{1,3} | latools/helpers/helpers.py | def analyte_2_massname(s):
"""
Converts analytes in format 'Al27' to '27Al'.
Parameters
----------
s : str
of format [0-9]{1,3}[A-z]{1,3}
Returns
-------
str
Name in format [A-z]{1,3}[0-9]{1,3}
"""
el = re.match('.*?([A-z]{1,3}).*?', s).groups()[0]
m = re.ma... | def analyte_2_massname(s):
"""
Converts analytes in format 'Al27' to '27Al'.
Parameters
----------
s : str
of format [0-9]{1,3}[A-z]{1,3}
Returns
-------
str
Name in format [A-z]{1,3}[0-9]{1,3}
"""
el = re.match('.*?([A-z]{1,3}).*?', s).groups()[0]
m = re.ma... | [
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] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/helpers/helpers.py#L168-L185 | [
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test | collate_data | Copy all csvs in nested directroy to single directory.
Function to copy all csvs from a directory, and place
them in a new directory.
Parameters
----------
in_dir : str
Input directory containing csv files in subfolders
extension : str
The extension that identifies your data fi... | latools/helpers/helpers.py | def collate_data(in_dir, extension='.csv', out_dir=None):
"""
Copy all csvs in nested directroy to single directory.
Function to copy all csvs from a directory, and place
them in a new directory.
Parameters
----------
in_dir : str
Input directory containing csv files in subfolders
... | def collate_data(in_dir, extension='.csv', out_dir=None):
"""
Copy all csvs in nested directroy to single directory.
Function to copy all csvs from a directory, and place
them in a new directory.
Parameters
----------
in_dir : str
Input directory containing csv files in subfolders
... | [
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] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/helpers/helpers.py#L187-L218 | [
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test | bool_2_indices | Convert boolean array into a 2D array of (start, stop) pairs. | latools/helpers/helpers.py | def bool_2_indices(a):
"""
Convert boolean array into a 2D array of (start, stop) pairs.
"""
if any(a):
lims = []
lims.append(np.where(a[:-1] != a[1:])[0])
if a[0]:
lims.append([0])
if a[-1]:
lims.append([len(a) - 1])
lims = np.concatenate... | def bool_2_indices(a):
"""
Convert boolean array into a 2D array of (start, stop) pairs.
"""
if any(a):
lims = []
lims.append(np.where(a[:-1] != a[1:])[0])
if a[0]:
lims.append([0])
if a[-1]:
lims.append([len(a) - 1])
lims = np.concatenate... | [
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test | enumerate_bool | Consecutively numbers contiguous booleans in array.
i.e. a boolean sequence, and resulting numbering
T F T T T F T F F F T T F
0-1 1 1 - 2 ---3 3 -
where ' - '
Parameters
----------
bool_array : array_like
Array of booleans.
nstart : int
The number of the first boolean... | latools/helpers/helpers.py | def enumerate_bool(bool_array, nstart=0):
"""
Consecutively numbers contiguous booleans in array.
i.e. a boolean sequence, and resulting numbering
T F T T T F T F F F T T F
0-1 1 1 - 2 ---3 3 -
where ' - '
Parameters
----------
bool_array : array_like
Array of booleans.
... | def enumerate_bool(bool_array, nstart=0):
"""
Consecutively numbers contiguous booleans in array.
i.e. a boolean sequence, and resulting numbering
T F T T T F T F F F T T F
0-1 1 1 - 2 ---3 3 -
where ' - '
Parameters
----------
bool_array : array_like
Array of booleans.
... | [
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] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/helpers/helpers.py#L239-L260 | [
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test | tuples_2_bool | Generate boolean array from list of limit tuples.
Parameters
----------
tuples : array_like
[2, n] array of (start, end) values
x : array_like
x scale the tuples are mapped to
Returns
-------
array_like
boolean array, True where x is between each pair of tuples. | latools/helpers/helpers.py | def tuples_2_bool(tuples, x):
"""
Generate boolean array from list of limit tuples.
Parameters
----------
tuples : array_like
[2, n] array of (start, end) values
x : array_like
x scale the tuples are mapped to
Returns
-------
array_like
boolean array, True w... | def tuples_2_bool(tuples, x):
"""
Generate boolean array from list of limit tuples.
Parameters
----------
tuples : array_like
[2, n] array of (start, end) values
x : array_like
x scale the tuples are mapped to
Returns
-------
array_like
boolean array, True w... | [
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] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/helpers/helpers.py#L262-L284 | [
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test | rolling_window | Returns (win, len(a)) rolling - window array of data.
Parameters
----------
a : array_like
Array to calculate the rolling window of
window : int
Description of `window`.
pad : same as dtype(a)
Description of `pad`.
Returns
-------
array_like
An array of ... | latools/helpers/helpers.py | def rolling_window(a, window, pad=None):
"""
Returns (win, len(a)) rolling - window array of data.
Parameters
----------
a : array_like
Array to calculate the rolling window of
window : int
Description of `window`.
pad : same as dtype(a)
Description of `pad`.
Re... | def rolling_window(a, window, pad=None):
"""
Returns (win, len(a)) rolling - window array of data.
Parameters
----------
a : array_like
Array to calculate the rolling window of
window : int
Description of `window`.
pad : same as dtype(a)
Description of `pad`.
Re... | [
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"-",
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] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/helpers/helpers.py#L328-L377 | [
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test | fastsmooth | Returns rolling - window smooth of a.
Function to efficiently calculate the rolling mean of a numpy
array using 'stride_tricks' to split up a 1D array into an ndarray of
sub - sections of the original array, of dimensions [len(a) - win, win].
Parameters
----------
a : array_like
The 1D... | latools/helpers/helpers.py | def fastsmooth(a, win=11):
"""
Returns rolling - window smooth of a.
Function to efficiently calculate the rolling mean of a numpy
array using 'stride_tricks' to split up a 1D array into an ndarray of
sub - sections of the original array, of dimensions [len(a) - win, win].
Parameters
-----... | def fastsmooth(a, win=11):
"""
Returns rolling - window smooth of a.
Function to efficiently calculate the rolling mean of a numpy
array using 'stride_tricks' to split up a 1D array into an ndarray of
sub - sections of the original array, of dimensions [len(a) - win, win].
Parameters
-----... | [
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test | fastgrad | Returns rolling - window gradient of a.
Function to efficiently calculate the rolling gradient of a numpy
array using 'stride_tricks' to split up a 1D array into an ndarray of
sub - sections of the original array, of dimensions [len(a) - win, win].
Parameters
----------
a : array_like
... | latools/helpers/helpers.py | def fastgrad(a, win=11):
"""
Returns rolling - window gradient of a.
Function to efficiently calculate the rolling gradient of a numpy
array using 'stride_tricks' to split up a 1D array into an ndarray of
sub - sections of the original array, of dimensions [len(a) - win, win].
Parameters
-... | def fastgrad(a, win=11):
"""
Returns rolling - window gradient of a.
Function to efficiently calculate the rolling gradient of a numpy
array using 'stride_tricks' to split up a 1D array into an ndarray of
sub - sections of the original array, of dimensions [len(a) - win, win].
Parameters
-... | [
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] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/helpers/helpers.py#L408-L439 | [
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test | calc_grads | Calculate gradients of values in dat.
Parameters
----------
x : array like
Independent variable for items in dat.
dat : dict
{key: dependent_variable} pairs
keys : str or array-like
Which keys in dict to calculate the gradient of.
win : int
The side of the ro... | latools/helpers/helpers.py | def calc_grads(x, dat, keys=None, win=5):
"""
Calculate gradients of values in dat.
Parameters
----------
x : array like
Independent variable for items in dat.
dat : dict
{key: dependent_variable} pairs
keys : str or array-like
Which keys in dict to calculate the... | def calc_grads(x, dat, keys=None, win=5):
"""
Calculate gradients of values in dat.
Parameters
----------
x : array like
Independent variable for items in dat.
dat : dict
{key: dependent_variable} pairs
keys : str or array-like
Which keys in dict to calculate the... | [
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... | cd25a650cfee318152f234d992708511f7047fbe |
test | findmins | Function to find local minima.
Parameters
----------
x, y : array_like
1D arrays of the independent (x) and dependent (y) variables.
Returns
-------
array_like
Array of points in x where y has a local minimum. | latools/helpers/helpers.py | def findmins(x, y):
""" Function to find local minima.
Parameters
----------
x, y : array_like
1D arrays of the independent (x) and dependent (y) variables.
Returns
-------
array_like
Array of points in x where y has a local minimum.
"""
return x[np.r_[False, y[1:] ... | def findmins(x, y):
""" Function to find local minima.
Parameters
----------
x, y : array_like
1D arrays of the independent (x) and dependent (y) variables.
Returns
-------
array_like
Array of points in x where y has a local minimum.
"""
return x[np.r_[False, y[1:] ... | [
"Function",
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] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/helpers/helpers.py#L481-L494 | [
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... | cd25a650cfee318152f234d992708511f7047fbe |
test | stack_keys | Combine elements of ddict into an array of shape (len(ddict[key]), len(keys)).
Useful for preparing data for sklearn.
Parameters
----------
ddict : dict
A dict containing arrays or lists to be stacked.
Must be of equal length.
keys : list or str
The keys of dict to stack. M... | latools/helpers/helpers.py | def stack_keys(ddict, keys, extra=None):
"""
Combine elements of ddict into an array of shape (len(ddict[key]), len(keys)).
Useful for preparing data for sklearn.
Parameters
----------
ddict : dict
A dict containing arrays or lists to be stacked.
Must be of equal length.
ke... | def stack_keys(ddict, keys, extra=None):
"""
Combine elements of ddict into an array of shape (len(ddict[key]), len(keys)).
Useful for preparing data for sklearn.
Parameters
----------
ddict : dict
A dict containing arrays or lists to be stacked.
Must be of equal length.
ke... | [
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test | cluster_meanshift | Identify clusters using Meanshift algorithm.
Parameters
----------
data : array_like
array of size [n_samples, n_features].
bandwidth : float or None
If None, bandwidth is estimated automatically using
sklean.cluster.estimate_bandwidth
bin_seeding : bool
Setting this... | latools/filtering/clustering.py | def cluster_meanshift(data, bandwidth=None, bin_seeding=False, **kwargs):
"""
Identify clusters using Meanshift algorithm.
Parameters
----------
data : array_like
array of size [n_samples, n_features].
bandwidth : float or None
If None, bandwidth is estimated automatically using... | def cluster_meanshift(data, bandwidth=None, bin_seeding=False, **kwargs):
"""
Identify clusters using Meanshift algorithm.
Parameters
----------
data : array_like
array of size [n_samples, n_features].
bandwidth : float or None
If None, bandwidth is estimated automatically using... | [
"Identify",
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] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/filtering/clustering.py#L5-L33 | [
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... | cd25a650cfee318152f234d992708511f7047fbe |
test | cluster_kmeans | Identify clusters using K - Means algorithm.
Parameters
----------
data : array_like
array of size [n_samples, n_features].
n_clusters : int
The number of clusters expected in the data.
Returns
-------
dict
boolean array for each identified cluster. | latools/filtering/clustering.py | def cluster_kmeans(data, n_clusters, **kwargs):
"""
Identify clusters using K - Means algorithm.
Parameters
----------
data : array_like
array of size [n_samples, n_features].
n_clusters : int
The number of clusters expected in the data.
Returns
-------
dict
... | def cluster_kmeans(data, n_clusters, **kwargs):
"""
Identify clusters using K - Means algorithm.
Parameters
----------
data : array_like
array of size [n_samples, n_features].
n_clusters : int
The number of clusters expected in the data.
Returns
-------
dict
... | [
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test | cluster_DBSCAN | Identify clusters using DBSCAN algorithm.
Parameters
----------
data : array_like
array of size [n_samples, n_features].
eps : float
The minimum 'distance' points must be apart for them to be in the
same cluster. Defaults to 0.3. Note: If the data are normalised
(they sh... | latools/filtering/clustering.py | def cluster_DBSCAN(data, eps=None, min_samples=None,
n_clusters=None, maxiter=200, **kwargs):
"""
Identify clusters using DBSCAN algorithm.
Parameters
----------
data : array_like
array of size [n_samples, n_features].
eps : float
The minimum 'distance' points... | def cluster_DBSCAN(data, eps=None, min_samples=None,
n_clusters=None, maxiter=200, **kwargs):
"""
Identify clusters using DBSCAN algorithm.
Parameters
----------
data : array_like
array of size [n_samples, n_features].
eps : float
The minimum 'distance' points... | [
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] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/filtering/clustering.py#L58-L123 | [
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test | get_defined_srms | Returns list of SRMS defined in the SRM database | latools/helpers/srm.py | def get_defined_srms(srm_file):
"""
Returns list of SRMS defined in the SRM database
"""
srms = read_table(srm_file)
return np.asanyarray(srms.index.unique()) | def get_defined_srms(srm_file):
"""
Returns list of SRMS defined in the SRM database
"""
srms = read_table(srm_file)
return np.asanyarray(srms.index.unique()) | [
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test | read_configuration | Read LAtools configuration file, and return parameters as dict. | latools/helpers/config.py | def read_configuration(config='DEFAULT'):
"""
Read LAtools configuration file, and return parameters as dict.
"""
# read configuration file
_, conf = read_latoolscfg()
# if 'DEFAULT', check which is the default configuration
if config == 'DEFAULT':
config = conf['DEFAULT']['config']
... | def read_configuration(config='DEFAULT'):
"""
Read LAtools configuration file, and return parameters as dict.
"""
# read configuration file
_, conf = read_latoolscfg()
# if 'DEFAULT', check which is the default configuration
if config == 'DEFAULT':
config = conf['DEFAULT']['config']
... | [
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] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/helpers/config.py#L13-L27 | [
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test | read_latoolscfg | Reads configuration, returns a ConfigParser object.
Distinct from read_configuration, which returns a dict. | latools/helpers/config.py | def read_latoolscfg():
"""
Reads configuration, returns a ConfigParser object.
Distinct from read_configuration, which returns a dict.
"""
config_file = pkgrs.resource_filename('latools', 'latools.cfg')
cf = configparser.ConfigParser()
cf.read(config_file)
return config_file, cf | def read_latoolscfg():
"""
Reads configuration, returns a ConfigParser object.
Distinct from read_configuration, which returns a dict.
"""
config_file = pkgrs.resource_filename('latools', 'latools.cfg')
cf = configparser.ConfigParser()
cf.read(config_file)
return config_file, cf | [
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test | print_all | Prints all currently defined configurations. | latools/helpers/config.py | def print_all():
"""
Prints all currently defined configurations.
"""
# read configuration file
_, conf = read_latoolscfg()
default = conf['DEFAULT']['config']
pstr = '\nCurrently defined LAtools configurations:\n\n'
for s in conf.sections():
if s == default:
pstr +... | def print_all():
"""
Prints all currently defined configurations.
"""
# read configuration file
_, conf = read_latoolscfg()
default = conf['DEFAULT']['config']
pstr = '\nCurrently defined LAtools configurations:\n\n'
for s in conf.sections():
if s == default:
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test | copy_SRM_file | Creates a copy of the default SRM table at the specified location.
Parameters
----------
destination : str
The save location for the SRM file. If no location specified,
saves it as 'LAtools_[config]_SRMTable.csv' in the current working
directory.
config : str
It's poss... | latools/helpers/config.py | def copy_SRM_file(destination=None, config='DEFAULT'):
"""
Creates a copy of the default SRM table at the specified location.
Parameters
----------
destination : str
The save location for the SRM file. If no location specified,
saves it as 'LAtools_[config]_SRMTable.csv' in the cur... | def copy_SRM_file(destination=None, config='DEFAULT'):
"""
Creates a copy of the default SRM table at the specified location.
Parameters
----------
destination : str
The save location for the SRM file. If no location specified,
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test | create | Adds a new configuration to latools.cfg.
Parameters
----------
config_name : str
The name of the new configuration. This should be descriptive
(e.g. UC Davis Foram Group)
srmfile : str (optional)
The location of the srm file used for calibration.
dataformat : str (optional)
... | latools/helpers/config.py | def create(config_name, srmfile=None, dataformat=None, base_on='DEFAULT', make_default=False):
"""
Adds a new configuration to latools.cfg.
Parameters
----------
config_name : str
The name of the new configuration. This should be descriptive
(e.g. UC Davis Foram Group)
srmfile :... | def create(config_name, srmfile=None, dataformat=None, base_on='DEFAULT', make_default=False):
"""
Adds a new configuration to latools.cfg.
Parameters
----------
config_name : str
The name of the new configuration. This should be descriptive
(e.g. UC Davis Foram Group)
srmfile :... | [
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test | change_default | Change the default configuration. | latools/helpers/config.py | def change_default(config):
"""
Change the default configuration.
"""
config_file, cf = read_latoolscfg()
if config not in cf.sections():
raise ValueError("\n'{:s}' is not a defined configuration.".format(config))
if config == 'REPRODUCE':
pstr = ('Are you SURE you want to set ... | def change_default(config):
"""
Change the default configuration.
"""
config_file, cf = read_latoolscfg()
if config not in cf.sections():
raise ValueError("\n'{:s}' is not a defined configuration.".format(config))
if config == 'REPRODUCE':
pstr = ('Are you SURE you want to set ... | [
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test | threshold | Return boolean arrays where a >= and < threshold.
Parameters
----------
values : array-like
Array of real values.
threshold : float
Threshold value
Returns
-------
(below, above) : tuple or boolean arrays | latools/filtering/filters.py | def threshold(values, threshold):
"""
Return boolean arrays where a >= and < threshold.
Parameters
----------
values : array-like
Array of real values.
threshold : float
Threshold value
Returns
-------
(below, above) : tuple or boolean arrays
"""
values ... | def threshold(values, threshold):
"""
Return boolean arrays where a >= and < threshold.
Parameters
----------
values : array-like
Array of real values.
threshold : float
Threshold value
Returns
-------
(below, above) : tuple or boolean arrays
"""
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test | exclude_downhole | Exclude all data after the first excluded portion.
This makes sense for spot measurements where, because
of the signal mixing inherent in LA-ICPMS, once a
contaminant is ablated, it will always be present to
some degree in signals from further down the ablation
pit.
Parameters
----------
... | latools/filtering/filters.py | def exclude_downhole(filt, threshold=2):
"""
Exclude all data after the first excluded portion.
This makes sense for spot measurements where, because
of the signal mixing inherent in LA-ICPMS, once a
contaminant is ablated, it will always be present to
some degree in signals from further down t... | def exclude_downhole(filt, threshold=2):
"""
Exclude all data after the first excluded portion.
This makes sense for spot measurements where, because
of the signal mixing inherent in LA-ICPMS, once a
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test | defrag | 'Defragment' a filter.
Parameters
----------
filt : boolean array
A filter
threshold : int
Consecutive values equal to or below this threshold
length are considered fragments, and will be removed.
mode : str
Wheter to change False fragments to True ('include')
... | latools/filtering/filters.py | def defrag(filt, threshold=3, mode='include'):
"""
'Defragment' a filter.
Parameters
----------
filt : boolean array
A filter
threshold : int
Consecutive values equal to or below this threshold
length are considered fragments, and will be removed.
mode : str
... | def defrag(filt, threshold=3, mode='include'):
"""
'Defragment' a filter.
Parameters
----------
filt : boolean array
A filter
threshold : int
Consecutive values equal to or below this threshold
length are considered fragments, and will be removed.
mode : str
... | [
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test | trim | Remove points from the start and end of True regions.
Parameters
----------
start, end : int
The number of points to remove from the start and end of
the specified filter.
ind : boolean array
Which filter to trim. If True, applies to currently active
filters. | latools/filtering/filters.py | def trim(ind, start=1, end=0):
"""
Remove points from the start and end of True regions.
Parameters
----------
start, end : int
The number of points to remove from the start and end of
the specified filter.
ind : boolean array
Which filter to trim. If True, applies t... | def trim(ind, start=1, end=0):
"""
Remove points from the start and end of True regions.
Parameters
----------
start, end : int
The number of points to remove from the start and end of
the specified filter.
ind : boolean array
Which filter to trim. If True, applies t... | [
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test | D.setfocus | Set the 'focus' attribute of the data file.
The 'focus' attribute of the object points towards data from a
particular stage of analysis. It is used to identify the 'working
stage' of the data. Processing functions operate on the 'focus'
stage, so if steps are done out of sequence, thing... | latools/D_obj.py | def setfocus(self, focus):
"""
Set the 'focus' attribute of the data file.
The 'focus' attribute of the object points towards data from a
particular stage of analysis. It is used to identify the 'working
stage' of the data. Processing functions operate on the 'focus'
sta... | def setfocus(self, focus):
"""
Set the 'focus' attribute of the data file.
The 'focus' attribute of the object points towards data from a
particular stage of analysis. It is used to identify the 'working
stage' of the data. Processing functions operate on the 'focus'
sta... | [
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] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/D_obj.py#L155-L191 | [
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test | D.despike | Applies expdecay_despiker and noise_despiker to data.
Parameters
----------
expdecay_despiker : bool
Whether or not to apply the exponential decay filter.
exponent : None or float
The exponent for the exponential decay filter. If None,
it is determine... | latools/D_obj.py | def despike(self, expdecay_despiker=True, exponent=None,
noise_despiker=True, win=3, nlim=12., maxiter=3):
"""
Applies expdecay_despiker and noise_despiker to data.
Parameters
----------
expdecay_despiker : bool
Whether or not to apply the exponential... | def despike(self, expdecay_despiker=True, exponent=None,
noise_despiker=True, win=3, nlim=12., maxiter=3):
"""
Applies expdecay_despiker and noise_despiker to data.
Parameters
----------
expdecay_despiker : bool
Whether or not to apply the exponential... | [
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test | D.autorange | Automatically separates signal and background data regions.
Automatically detect signal and background regions in the laser
data, based on the behaviour of a single analyte. The analyte used
should be abundant and homogenous in the sample.
**Step 1: Thresholding.**
The backgrou... | latools/D_obj.py | def autorange(self, analyte='total_counts', gwin=5, swin=3, win=30,
on_mult=[1., 1.], off_mult=[1., 1.5],
ploterrs=True, transform='log', **kwargs):
"""
Automatically separates signal and background data regions.
Automatically detect signal and background reg... | def autorange(self, analyte='total_counts', gwin=5, swin=3, win=30,
on_mult=[1., 1.], off_mult=[1., 1.5],
ploterrs=True, transform='log', **kwargs):
"""
Automatically separates signal and background data regions.
Automatically detect signal and background reg... | [
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test | D.autorange_plot | Plot a detailed autorange report for this sample. | latools/D_obj.py | def autorange_plot(self, analyte='total_counts', gwin=7, swin=None, win=20,
on_mult=[1.5, 1.], off_mult=[1., 1.5],
transform='log'):
"""
Plot a detailed autorange report for this sample.
"""
if analyte is None:
# sig = self.focus[... | def autorange_plot(self, analyte='total_counts', gwin=7, swin=None, win=20,
on_mult=[1.5, 1.], off_mult=[1., 1.5],
transform='log'):
"""
Plot a detailed autorange report for this sample.
"""
if analyte is None:
# sig = self.focus[... | [
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test | D.mkrngs | Transform boolean arrays into list of limit pairs.
Gets Time limits of signal/background boolean arrays and stores them as
sigrng and bkgrng arrays. These arrays can be saved by 'save_ranges' in
the analyse object. | latools/D_obj.py | def mkrngs(self):
"""
Transform boolean arrays into list of limit pairs.
Gets Time limits of signal/background boolean arrays and stores them as
sigrng and bkgrng arrays. These arrays can be saved by 'save_ranges' in
the analyse object.
"""
bbool = bool_2_indices... | def mkrngs(self):
"""
Transform boolean arrays into list of limit pairs.
Gets Time limits of signal/background boolean arrays and stores them as
sigrng and bkgrng arrays. These arrays can be saved by 'save_ranges' in
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"""
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test | D.bkg_subtract | Subtract provided background from signal (focus stage).
Results is saved in new 'bkgsub' focus stage
Returns
-------
None | latools/D_obj.py | def bkg_subtract(self, analyte, bkg, ind=None, focus_stage='despiked'):
"""
Subtract provided background from signal (focus stage).
Results is saved in new 'bkgsub' focus stage
Returns
-------
None
"""
if 'bkgsub' not in self.data.keys():
sel... | def bkg_subtract(self, analyte, bkg, ind=None, focus_stage='despiked'):
"""
Subtract provided background from signal (focus stage).
Results is saved in new 'bkgsub' focus stage
Returns
-------
None
"""
if 'bkgsub' not in self.data.keys():
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test | D.correct_spectral_interference | Correct spectral interference.
Subtract interference counts from target_analyte, based on the
intensity of a source_analayte and a known fractional contribution (f).
Correction takes the form:
target_analyte -= source_analyte * f
Only operates on background-corrected data ('bk... | latools/D_obj.py | def correct_spectral_interference(self, target_analyte, source_analyte, f):
"""
Correct spectral interference.
Subtract interference counts from target_analyte, based on the
intensity of a source_analayte and a known fractional contribution (f).
Correction takes the form:
... | def correct_spectral_interference(self, target_analyte, source_analyte, f):
"""
Correct spectral interference.
Subtract interference counts from target_analyte, based on the
intensity of a source_analayte and a known fractional contribution (f).
Correction takes the form:
... | [
"Correct",
"spectral",
"interference",
"."
] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/D_obj.py#L430-L467 | [
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"'target_analyte: {:} not in available analytes ({:})'",... | cd25a650cfee318152f234d992708511f7047fbe |
test | D.ratio | Divide all analytes by a specified internal_standard analyte.
Parameters
----------
internal_standard : str
The analyte used as the internal_standard.
Returns
-------
None | latools/D_obj.py | def ratio(self, internal_standard=None):
"""
Divide all analytes by a specified internal_standard analyte.
Parameters
----------
internal_standard : str
The analyte used as the internal_standard.
Returns
-------
None
"""
if in... | def ratio(self, internal_standard=None):
"""
Divide all analytes by a specified internal_standard analyte.
Parameters
----------
internal_standard : str
The analyte used as the internal_standard.
Returns
-------
None
"""
if in... | [
"Divide",
"all",
"analytes",
"by",
"a",
"specified",
"internal_standard",
"analyte",
"."
] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/D_obj.py#L470-L491 | [
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test | D.calibrate | Apply calibration to data.
The `calib_dict` must be calculated at the `analyse` level,
and passed to this calibrate function.
Parameters
----------
calib_dict : dict
A dict of calibration values to apply to each analyte.
Returns
-------
None | latools/D_obj.py | def calibrate(self, calib_ps, analytes=None):
"""
Apply calibration to data.
The `calib_dict` must be calculated at the `analyse` level,
and passed to this calibrate function.
Parameters
----------
calib_dict : dict
A dict of calibration values to ap... | def calibrate(self, calib_ps, analytes=None):
"""
Apply calibration to data.
The `calib_dict` must be calculated at the `analyse` level,
and passed to this calibrate function.
Parameters
----------
calib_dict : dict
A dict of calibration values to ap... | [
"Apply",
"calibration",
"to",
"data",
"."
] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/D_obj.py#L494-L532 | [
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"not",
... | cd25a650cfee318152f234d992708511f7047fbe |
test | D.sample_stats | Calculate sample statistics
Returns samples, analytes, and arrays of statistics
of shape (samples, analytes). Statistics are calculated
from the 'focus' data variable, so output depends on how
the data have been processed.
Parameters
----------
analytes : array_... | latools/D_obj.py | def sample_stats(self, analytes=None, filt=True,
stat_fns={},
eachtrace=True):
"""
Calculate sample statistics
Returns samples, analytes, and arrays of statistics
of shape (samples, analytes). Statistics are calculated
from the 'focus' d... | def sample_stats(self, analytes=None, filt=True,
stat_fns={},
eachtrace=True):
"""
Calculate sample statistics
Returns samples, analytes, and arrays of statistics
of shape (samples, analytes). Statistics are calculated
from the 'focus' d... | [
"Calculate",
"sample",
"statistics"
] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/D_obj.py#L536-L590 | [
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"elif"... | cd25a650cfee318152f234d992708511f7047fbe |
test | D.ablation_times | Function for calculating the ablation time for each
ablation.
Returns
-------
dict of times for each ablation. | latools/D_obj.py | def ablation_times(self):
"""
Function for calculating the ablation time for each
ablation.
Returns
-------
dict of times for each ablation.
"""
ats = {}
for n in np.arange(self.n) + 1:
t = self.Time[self.ns == n]
ats[n... | def ablation_times(self):
"""
Function for calculating the ablation time for each
ablation.
Returns
-------
dict of times for each ablation.
"""
ats = {}
for n in np.arange(self.n) + 1:
t = self.Time[self.ns == n]
ats[n... | [
"Function",
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"the",
"ablation",
"time",
"for",
"each",
"ablation",
"."
] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/D_obj.py#L593-L606 | [
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"[",
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... | cd25a650cfee318152f234d992708511f7047fbe |
test | D.filter_threshold | Apply threshold filter.
Generates threshold filters for the given analytes above and below
the specified threshold.
Two filters are created with prefixes '_above' and '_below'.
'_above' keeps all the data above the threshold.
'_below' keeps all the data below the thresh... | latools/D_obj.py | def filter_threshold(self, analyte, threshold):
"""
Apply threshold filter.
Generates threshold filters for the given analytes above and below
the specified threshold.
Two filters are created with prefixes '_above' and '_below'.
'_above' keeps all the data above the... | def filter_threshold(self, analyte, threshold):
"""
Apply threshold filter.
Generates threshold filters for the given analytes above and below
the specified threshold.
Two filters are created with prefixes '_above' and '_below'.
'_above' keeps all the data above the... | [
"Apply",
"threshold",
"filter",
"."
] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/D_obj.py#L610-L650 | [
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"=",
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"threshold",
"(",
"self... | cd25a650cfee318152f234d992708511f7047fbe |
test | D.filter_gradient_threshold | Apply gradient threshold filter.
Generates threshold filters for the given analytes above and below
the specified threshold.
Two filters are created with prefixes '_above' and '_below'.
'_above' keeps all the data above the threshold.
'_below' keeps all the data below t... | latools/D_obj.py | def filter_gradient_threshold(self, analyte, win, threshold, recalc=True):
"""
Apply gradient threshold filter.
Generates threshold filters for the given analytes above and below
the specified threshold.
Two filters are created with prefixes '_above' and '_below'.
'... | def filter_gradient_threshold(self, analyte, win, threshold, recalc=True):
"""
Apply gradient threshold filter.
Generates threshold filters for the given analytes above and below
the specified threshold.
Two filters are created with prefixes '_above' and '_below'.
'... | [
"Apply",
"gradient",
"threshold",
"filter",
"."
] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/D_obj.py#L653-L702 | [
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"# calculate absolute gradient",
"if",
"r... | cd25a650cfee318152f234d992708511f7047fbe |
test | D.filter_clustering | Applies an n - dimensional clustering filter to the data.
Available Clustering Algorithms
* 'meanshift': The `sklearn.cluster.MeanShift` algorithm.
Automatically determines number of clusters
in data based on the `bandwidth` of expected
variation.
* 'kmeans': The ... | latools/D_obj.py | def filter_clustering(self, analytes, filt=False, normalise=True,
method='meanshift', include_time=False,
sort=None, min_data=10, **kwargs):
"""
Applies an n - dimensional clustering filter to the data.
Available Clustering Algorithms
... | def filter_clustering(self, analytes, filt=False, normalise=True,
method='meanshift', include_time=False,
sort=None, min_data=10, **kwargs):
"""
Applies an n - dimensional clustering filter to the data.
Available Clustering Algorithms
... | [
"Applies",
"an",
"n",
"-",
"dimensional",
"clustering",
"filter",
"to",
"the",
"data",
"."
] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/D_obj.py#L705-L912 | [
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",",
"*",
"*... | cd25a650cfee318152f234d992708511f7047fbe |
test | D.calc_correlation | Calculate local correlation between two analytes.
Parameters
----------
x_analyte, y_analyte : str
The names of the x and y analytes to correlate.
window : int, None
The rolling window used when calculating the correlation.
filt : bool
Whether... | latools/D_obj.py | def calc_correlation(self, x_analyte, y_analyte, window=15, filt=True, recalc=True):
"""
Calculate local correlation between two analytes.
Parameters
----------
x_analyte, y_analyte : str
The names of the x and y analytes to correlate.
window : int, None
... | def calc_correlation(self, x_analyte, y_analyte, window=15, filt=True, recalc=True):
"""
Calculate local correlation between two analytes.
Parameters
----------
x_analyte, y_analyte : str
The names of the x and y analytes to correlate.
window : int, None
... | [
"Calculate",
"local",
"correlation",
"between",
"two",
"analytes",
"."
] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/D_obj.py#L915-L963 | [
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"(",
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",",
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","... | cd25a650cfee318152f234d992708511f7047fbe |
test | D.filter_correlation | Calculate correlation filter.
Parameters
----------
x_analyte, y_analyte : str
The names of the x and y analytes to correlate.
window : int, None
The rolling window used when calculating the correlation.
r_threshold : float
The correlation ind... | latools/D_obj.py | def filter_correlation(self, x_analyte, y_analyte, window=15,
r_threshold=0.9, p_threshold=0.05, filt=True, recalc=False):
"""
Calculate correlation filter.
Parameters
----------
x_analyte, y_analyte : str
The names of the x and y analytes ... | def filter_correlation(self, x_analyte, y_analyte, window=15,
r_threshold=0.9, p_threshold=0.05, filt=True, recalc=False):
"""
Calculate correlation filter.
Parameters
----------
x_analyte, y_analyte : str
The names of the x and y analytes ... | [
"Calculate",
"correlation",
"filter",
"."
] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/D_obj.py#L966-L1021 | [
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"# make window odd",
... | cd25a650cfee318152f234d992708511f7047fbe |
test | D.correlation_plot | Plot the local correlation between two analytes.
Parameters
----------
x_analyte, y_analyte : str
The names of the x and y analytes to correlate.
window : int, None
The rolling window used when calculating the correlation.
filt : bool
Whether ... | latools/D_obj.py | def correlation_plot(self, x_analyte, y_analyte, window=15, filt=True, recalc=False):
"""
Plot the local correlation between two analytes.
Parameters
----------
x_analyte, y_analyte : str
The names of the x and y analytes to correlate.
window : int, None
... | def correlation_plot(self, x_analyte, y_analyte, window=15, filt=True, recalc=False):
"""
Plot the local correlation between two analytes.
Parameters
----------
x_analyte, y_analyte : str
The names of the x and y analytes to correlate.
window : int, None
... | [
"Plot",
"the",
"local",
"correlation",
"between",
"two",
"analytes",
"."
] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/D_obj.py#L1024-L1073 | [
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",... | cd25a650cfee318152f234d992708511f7047fbe |
test | D.filter_new | Make new filter from combination of other filters.
Parameters
----------
name : str
The name of the new filter. Should be unique.
filt_str : str
A logical combination of partial strings which will create
the new filter. For example, 'Albelow & Mnbelow... | latools/D_obj.py | def filter_new(self, name, filt_str):
"""
Make new filter from combination of other filters.
Parameters
----------
name : str
The name of the new filter. Should be unique.
filt_str : str
A logical combination of partial strings which will create
... | def filter_new(self, name, filt_str):
"""
Make new filter from combination of other filters.
Parameters
----------
name : str
The name of the new filter. Should be unique.
filt_str : str
A logical combination of partial strings which will create
... | [
"Make",
"new",
"filter",
"from",
"combination",
"of",
"other",
"filters",
"."
] | oscarbranson/latools | python | https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/D_obj.py#L1076-L1096 | [
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