def __init__(self, trajDataObj, eventProcHnd, eventPartitionSettings, eventProcSettings, settingsString):
"""
Initialize a new event segment object
"""
# Required arguments
self.trajDataObj=trajDataObj
self.eventProcHnd=eventProcHnd
# Reset function timer since esTimer is a class variable
partitionTimer.Reset()
self.settingsDict = eventPartitionSettings
self.eventProcSettingsDict = eventProcSettings
self.procTime=0.0
self.FsHz=self.trajDataObj.FsHz
self.DataLengthSec=self.trajDataObj.DataLengthSec
try:
self.writeEventTS=int(self.settingsDict.pop("writeEventTS",1))
self.parallelProc=int(self.settingsDict.pop("parallelProc",1))
self.reserveNCPU=int(self.settingsDict.pop("reserveNCPU",2))
except ValueError as err:
raise mosaic.commonExceptions.SettingsTypeError( err )
sys.stdout.flush()
self.tEventProcObj=self.eventProcHnd([], self.FsHz, eventstart=0,eventend=0, baselinestats=[ 0,0,0 ], algosettingsdict=self.eventProcSettingsDict.copy(), savets=False, absdatidx=0, datafileHnd=None )
self.mdioDBHnd=sqlite3MDIO.sqlite3MDIO()
self.mdioDBHnd.initDB(
dbPath=self.trajDataObj.datPath,
tableName='metadata',
colNames=(self.tEventProcObj.mdHeadings()),
colNames_t=(self.tEventProcObj.mdHeadingDataType())
)
self.mdioDBHnd.writeSettings(settingsString)
self.logger=mlog.mosaicLogging().getLogger(name=__name__, dbHnd=self.mdioDBHnd)
self.logger.debug(_d("Event Segment Initialization"))
self.logger.debug(_d("{0}", settingsString))
if self.trajDataObj.dataFilter:
self.fstring=type(self.trajDataObj.dataFilterObj).__name__
else:
self.fstring='None'
self._writeanalysisinfo()
if self.parallelProc:
self._setupparallel()
# Setup function timing
self.timingObj=mosaicTiming.mosaicTiming()
self._init(trajDataObj, eventProcHnd, eventPartitionSettings, eventProcSettings)
def __init__(self, parent = None):
self.v=[]
super(BlockDepthWindow, self).__init__(parent)
uic.loadUi(resource_path("blockdepthview.ui"), self)
self._positionWindow()
self.time=mosaicTiming.mosaicTiming()
self.queryInterval=5
self.lastQueryTime=round(self.time.time())
self.idleTimer=QtCore.QTimer()
self.idleTimer.start(3000)
self.queryString="select BlockDepth from metadata where ProcessingStatus='normal'and ResTime > 0.025"
self.queryData=[]
self.queryError=False
self.lastGoodQueryString=""
self.queryRunning=False
self.qWorker=None
self.qThread=QtCore.QThread()
self.queryCompleter=None
self.updateDataOnIdle=True
self.nBins=500
self.binsSpinBox.setValue(self.nBins)
# Set the default text in the Filter LineEdit
self.sqlQueryLineEdit.setCompleterValues([])
self.sqlQueryLineEdit.setText("ResTime > 0.025")
self.maxLevel=5
self.levelHorizontalSlider.setValue(self.maxLevel)
# add a status bar
sb=QtGui.QStatusBar()
self.statusBarHorizontalLayout.addWidget(sb)
self.statusBarHorizontalLayout.setMargin(0)
self.statusBarHorizontalLayout.setSpacing(0)
self.statusbarLine.hide()
QtCore.QObject.connect(self.updateButton, QtCore.SIGNAL('clicked()'), self.OnUpdateButton)
QtCore.QObject.connect(self.sqlQueryLineEdit, QtCore.SIGNAL('textChanged ( const QString & )'), self.OnQueryTextChange)
QtCore.QObject.connect(self.binsSpinBox, QtCore.SIGNAL('valueChanged ( int )'), self.OnBinsChange)
QtCore.QObject.connect(self.levelHorizontalSlider, QtCore.SIGNAL('valueChanged ( int )'), self.OnlevelSliderChange)
QtCore.QObject.connect(self.peakDetectCheckBox, QtCore.SIGNAL('clicked(bool)'), self.OnPeakDetect)
def __init__(self, icurr, icurrU, Fs, **kwargs):
"""
Store a ref to the raw event data.
"""
self.eventData=icurr
self.eventDataU=icurrU
self.Fs=Fs
self.logger=mlog.mosaicLogging().getLogger(name=__name__)
# Will throw a key error if not passed
self.eStartEstimate=kwargs['eventstart']
self.eEndEstimate=kwargs['eventend']
self.settingsDict=kwargs['algosettingsdict']
self.absDataStartIndex=kwargs['absdatidx']
[ self.baseMean, self.baseSD, self.baseSlope ]=kwargs['baselinestats']
self.saveTS=kwargs['savets']
# Optional args. If dataFileHnd is not passed at init, it must be set later
# If not set before WriteEvent is called, it will result in a MissingMDIOError
self.dataFileHnd=kwargs.pop("datafilehnd", None)
# self.dataFileHnd=kwargs['datafileHnd']
# meta-data attrs that are common to all event processing
self.mdProcessingStatus='normal'
# Setup function timing
self.timingObj=mosaicTiming.mosaicTiming()
self.mdEventProcessTime=0.0
# print self.settingsDict
# Call sub-class initialization
self._init(**kwargs)
def __init__(self, icurr, icurrU, Fs, **kwargs):
"""
Store a ref to the raw event data.
"""
self.eventData = icurr
self.eventDataU = icurrU
self.Fs = Fs
self.logger = mlog.mosaicLogging().getLogger(name=__name__)
# Will throw a key error if not passed
self.eStartEstimate = kwargs['eventstart']
self.eEndEstimate = kwargs['eventend']
self.settingsDict = kwargs['algosettingsdict']
self.absDataStartIndex = kwargs['absdatidx']
[self.baseMean, self.baseSD, self.baseSlope] = kwargs['baselinestats']
self.saveTS = kwargs['savets']
# Optional args. If dataFileHnd is not passed at init, it must be set later
# If not set before WriteEvent is called, it will result in a MissingMDIOError
self.dataFileHnd = kwargs.pop("datafilehnd", None)
# self.dataFileHnd=kwargs['datafileHnd']
# meta-data attrs that are common to all event processing
self.mdProcessingStatus = 'normal'
# Setup function timing
self.timingObj = mosaicTiming.mosaicTiming()
self.mdEventProcessTime = 0.0
# print self.settingsDict
# Call sub-class initialization
self._init(**kwargs)
def __init__(self, trajDataObj, eventProcHnd, eventPartitionSettings, eventProcSettings, settingsString, **kwargs):
"""
Initialize a new event segment object
"""
# Required arguments
self.trajDataObj=trajDataObj
self.eventProcHnd=eventProcHnd
# Reset function timer since esTimer is a class variable
partitionTimer.Reset()
self.settingsDict = eventPartitionSettings
self.eventProcSettingsDict = eventProcSettings
self.procTime=0.0
self.FsHz=self.trajDataObj.FsHz
self.DataLengthSec=self.trajDataObj.DataLengthSec
try:
self.writeEventTS=int(self.settingsDict.pop("writeEventTS",1))
self.parallelProc=int(self.settingsDict.pop("parallelProc",1))
self.reserveNCPU=int(self.settingsDict.pop("reserveNCPU",2))
self.driftThreshold=float(self.settingsDict.pop("driftThreshold",2.0))
self.maxDriftRate=float(self.settingsDict.pop("maxDriftRate",2.0))
self.minBaseline=float(self.settingsDict.pop("minBaseline",-1.))
self.maxBaseline=float(self.settingsDict.pop("maxBaseline",-1.))
except ValueError as err:
raise mosaic.commonExceptions.SettingsTypeError( err )
sys.stdout.flush()
self.tEventProcObj=self.eventProcHnd([], [], self.FsHz, eventstart=0,eventend=0, baselinestats=[ 0,0,0 ], algosettingsdict=self.eventProcSettingsDict.copy(), savets=False, absdatidx=0, datafileHnd=None )
self.mdioDBHnd=sqlite3MDIO.sqlite3MDIO()
self.mdioDBHnd.initDB(
dbPath=self.trajDataObj.datPath,
tableName='metadata',
colNames=(self.tEventProcObj.mdHeadings()),
colNames_t=(self.tEventProcObj.mdHeadingDataType()),
dbFilename=kwargs.get('dbFilename', '')
)
self.mdioDBHnd.writeSettings(settingsString)
self.logger=mlog.mosaicLogging().getLogger(name=__name__, dbHnd=self.mdioDBHnd)
self.logger.debug(_d("Event Segment Initialization"))
self.logger.debug(_d("{0}", settingsString))
if self.trajDataObj.dataFilter:
self.fstring=type(self.trajDataObj.dataFilterObj).__name__
else:
self.fstring='None'
self._writeanalysisinfo()
if self.parallelProc:
self._setupparallel()
# Setup function timing
self.timingObj=mosaicTiming.mosaicTiming()
self._init(trajDataObj, eventProcHnd, eventPartitionSettings, eventProcSettings)
import scipy.stats import uncertainties from collections import deque import mosaic.commonExceptions import mosaic.trajio.metaTrajIO as metaTrajIO import mosaic.mdio.sqlite3MDIO as sqlite3MDIO from mosaic.utilities.resource_path import format_path from mosaic.utilities.ionic_current_stats import OpenCurrentDist import mosaic.utilities.mosaicTiming as mosaicTiming import mosaic.utilities.mosaicLogging as mlog from mosaic.utilities.mosaicLogFormat import _d __all__ = ["metaEventPartition", "ExcessiveDriftError", "DriftRateError"] partitionTimer=mosaicTiming.mosaicTiming() # custom errors class ExcessiveDriftError(Exception): pass class DriftRateError(Exception): pass class metaEventPartition(object): """ .. warning:: |metaclass| A class to abstract partitioning individual events. Once a single molecule event is identified, it is handed off to to an event processor. If parallel processing is requested, detailed event processing will commence
pass
class SamplingRateChangedError(Exception):
pass
class EmptyDataPipeError(Exception):
pass
class FileNotFoundError(Exception):
pass
trajTimer = mtime.mosaicTiming()
ignorelist = ["eventProcessing*.log", "*.sqlite"]
class metaTrajIO(object):
"""
.. warning:: |metaclass|
Initialize a TrajIO object. The object can load all the data in a directory,
N files from a directory or from an explicit list of filenames. In addition
to the arguments defined below, implementations of this meta class may require
the definition of additional arguments. See the documentation of those classes
for what those may be. For example, the qdfTrajIO implementation of metaTrajIO also requires
the feedback resistance (Rfb) and feedback capacitance (Cfb) to be passed at initialization.
import scipy.stats import uncertainties from collections import deque import mosaic.commonExceptions import mosaic.trajio.metaTrajIO as metaTrajIO import mosaic.mdio.sqlite3MDIO as sqlite3MDIO from mosaic.utilities.resource_path import format_path from mosaic.utilities.ionic_current_stats import OpenCurrentDist import mosaic.utilities.mosaicTiming as mosaicTiming import mosaic.utilities.mosaicLogging as mlog from mosaic.utilities.mosaicLogFormat import _d __all__ = ["metaEventPartition", "ExcessiveDriftError", "DriftRateError"] partitionTimer=mosaicTiming.mosaicTiming() # custom errors class ExcessiveDriftError(Exception): pass class DriftRateError(Exception): pass class metaEventPartition(object): """ .. warning:: |metaclass| A class to abstract partitioning individual events. Once a single molecule event is identified, it is handed off to to an event processor. If parallel processing is requested, detailed event processing will commence
def __init__(self): self.pid=os.getpid() # Setup function timing self.timingObj=mosaicTiming.mosaicTiming()
class IncompatibleArgumentsError(Exception): pass class InsufficientArgumentsError(Exception): pass class IncorrectDataFormat(Exception): pass class EndOfFileError(Exception): pass class SamplingRateChangedError(Exception): pass class EmptyDataPipeError(Exception): pass class FileNotFoundError(Exception): pass trajTimer=mtime.mosaicTiming() ignorelist=[ "eventProcessing*.log", "*.sqlite" ] class metaTrajIO(object): """ .. warning:: |metaclass| Initialize a TrajIO object. The object can load all the data in a directory, N files from a directory or from an explicit list of filenames. In addition to the arguments defined below, implementations of this meta class may require the definition of additional arguments. See the documentation of those classes for what those may be. For example, the qdfTrajIO implementation of metaTrajIO also requires
def __init__(self, parent=None):
self.v = []
super(BlockDepthWindow, self).__init__(parent)
uic.loadUi(resource_path("blockdepthview.ui"), self)
self._positionWindow()
self.time = mosaicTiming.mosaicTiming()
self.queryInterval = 5
self.lastQueryTime = round(self.time.time())
self.idleTimer = QtCore.QTimer()
self.idleTimer.start(3000)
self.queryString = "select BlockDepth from metadata where ProcessingStatus='normal'and ResTime > 0.025"
self.queryData = []
self.queryError = False
self.lastGoodQueryString = ""
self.queryRunning = False
self.qWorker = None
self.qThread = QtCore.QThread()
self.queryCompleter = None
self.updateDataOnIdle = True
self.nBins = 500
self.binsSpinBox.setValue(self.nBins)
# Set the default text in the Filter LineEdit
self.sqlQueryLineEdit.setCompleterValues([])
self.sqlQueryLineEdit.setText("ResTime > 0.025")
self.maxLevel = 5
self.levelHorizontalSlider.setValue(self.maxLevel)
# add a status bar
sb = QtGui.QStatusBar()
self.statusBarHorizontalLayout.addWidget(sb)
self.statusBarHorizontalLayout.setMargin(0)
self.statusBarHorizontalLayout.setSpacing(0)
self.statusbarLine.hide()
QtCore.QObject.connect(self.updateButton, QtCore.SIGNAL('clicked()'),
self.OnUpdateButton)
QtCore.QObject.connect(
self.sqlQueryLineEdit,
QtCore.SIGNAL('textChanged ( const QString & )'),
self.OnQueryTextChange)
QtCore.QObject.connect(self.binsSpinBox,
QtCore.SIGNAL('valueChanged ( int )'),
self.OnBinsChange)
QtCore.QObject.connect(self.levelHorizontalSlider,
QtCore.SIGNAL('valueChanged ( int )'),
self.OnlevelSliderChange)
QtCore.QObject.connect(self.peakDetectCheckBox,
QtCore.SIGNAL('clicked(bool)'),
self.OnPeakDetect)
def __init__(self):
self.pid = os.getpid()
# Setup function timing
self.timingObj = mosaicTiming.mosaicTiming()
