baseUserAnalysis

Classes¤

`baseUserAnalysis` ¤

Create a userAnalysis object after bAnalysis has been analyzed with the core analysis results.

Source code in sanpy/user_analysis/baseUserAnalysis.py

class baseUserAnalysis:
    """Create a userAnalysis object after bAnalysis has been analyzed with the core analysis results."""

    def __init__(self, ba: "sanpy.bAnalysis"):
        self._myAnalysis: sanpy.bAnalysis = ba

        self._userStatDict: dict = {}
        # add to this with addUserStat()

        self.defineUserStats()

    def _getUserStatDict(self):
        """Get dict of user defined stats, one key per stat."""
        return self._userStatDict

    def defineUserStats(self):
        """Derived classes add each stat with addUserStat().

        See Also
        --------
        addUserStat
        """
        pass

    def addUserStat(self, humanName: str, internalName: str):
        """Add a user stat. Derived classes do this in defineUserStats().

        Parameters
        ----------
        humanName : str
            Human readable name for the stat, like 'Threshold Potential (mV)'
        internalName : str
            Name to use for the variable name of the stat.
            Should not contain special characters like space or '-'
            Can contain '_'

        Notes
        -----
        userStatDict = {
            'User Time To Peak (ms)' : {
                'name': 'user_timeToPeak_ms',
                'units': 'ms',
                'yStat': 'user_timeToPeak_ms',
                'yStatUnits': 'ms',
                'xStat': 'thresholdPnt',
                'xStatUnits': 'Points'
                }
        }
        """
        if humanName in self._userStatDict.keys():
            # logger.error(f'User stat with human name "{humanName}" already exists')
            return
        statDict = {
            "name": internalName,
            "units": None,
            "yStat": None,
            "yStatUnits": None,
            "xStat": None,
            "xStatUnits": None,
        }
        self._userStatDict[humanName] = statDict

    @property
    def ba(self):
        """Get the underlying [sanpy.bAnalysis][sanpy.bAnalysis] object"""
        return self._myAnalysis

    def getSweepX(self):
        """Get the x-axis of a recording."""
        return self.ba.fileLoader.sweepX

    def getSweepY(self):
        """Get the y-axis of a recording."""
        return self.ba.fileLoader.sweepY

    def getSweepC(self):
        """Get the DAC axis of a recording."""
        return self.ba.fileLoader.sweepC

    def getFilteredVm(self):
        return self.ba.fileLoader.sweepY_filtered

    def setSpikeValue(self, spikeIdx, theKey, theVal):
        """Set the value of a spike key.

        Parameters
        ----------
        spikeIdx : int
            The spike index , 0 based.
        theKey : str
            Name of the user defined internal name.
        theVal :
            The value for the key, can be almost any type like
            (float, int, bool, dict, list)

        Raises
        ------
        KeyError
            If theKey is not a key in analysis results.
        IndexError
            If spikeIdx is beyond number of spikes -1.
        """
        try:
            self.ba.spikeDict[spikeIdx][theKey] = theVal
        except (KeyError) as e:
            logger.error(f'User internal stat does not exist "{theKey}"')
        except (IndexError) as e:
            logger.error(
                f"spikeIdx {spikeIdx} is out of range, max value is {self.ba.numSpikes}"
            )

    def getSpikeValue(self, spikeIdx, theKey):
        """Get a single spike analysis result from key.

        Parameters
        ----------
        spikeIdx : int
            The spike index, 0 based.
        theKey : str
            Name of the analysis result defined internal name.

        Raises
        ------
        KeyError
            If theKey is not a key in analysis results.
        IndexError
            If spikeIdx is beyond number of spikes -1.
        """
        try:
            theRet = self.ba.spikeDict[spikeIdx][theKey]
            return theRet
        except KeyError as e:
            logger.error(f'User internal stat does not exist "{theKey}"')
        except IndexError as e:
            logger.error(
                f"spikeIdx {spikeIdx} is out of range, max value is {self.ba.numSpikes}"
            )

    def run(self):
        """Run user analysis. Calculate values for each new user stat."""

Attributes¤

`ba` `property` ¤

Get the underlying sanpy.bAnalysis object

Functions¤

`addUserStat(humanName, internalName)` ¤

Add a user stat. Derived classes do this in defineUserStats().

Parameters:

Name	Type	Description	Default
`humanName`	`str`	Human readable name for the stat, like 'Threshold Potential (mV)'	required
`internalName`	`str`	Name to use for the variable name of the stat. Should not contain special characters like space or '-' Can contain '_'	required

Notes¤

userStatDict = { 'User Time To Peak (ms)' : { 'name': 'user_timeToPeak_ms', 'units': 'ms', 'yStat': 'user_timeToPeak_ms', 'yStatUnits': 'ms', 'xStat': 'thresholdPnt', 'xStatUnits': 'Points' } }

Source code in sanpy/user_analysis/baseUserAnalysis.py

def addUserStat(self, humanName: str, internalName: str):
    """Add a user stat. Derived classes do this in defineUserStats().

    Parameters
    ----------
    humanName : str
        Human readable name for the stat, like 'Threshold Potential (mV)'
    internalName : str
        Name to use for the variable name of the stat.
        Should not contain special characters like space or '-'
        Can contain '_'

    Notes
    -----
    userStatDict = {
        'User Time To Peak (ms)' : {
            'name': 'user_timeToPeak_ms',
            'units': 'ms',
            'yStat': 'user_timeToPeak_ms',
            'yStatUnits': 'ms',
            'xStat': 'thresholdPnt',
            'xStatUnits': 'Points'
            }
    }
    """
    if humanName in self._userStatDict.keys():
        # logger.error(f'User stat with human name "{humanName}" already exists')
        return
    statDict = {
        "name": internalName,
        "units": None,
        "yStat": None,
        "yStatUnits": None,
        "xStat": None,
        "xStatUnits": None,
    }
    self._userStatDict[humanName] = statDict

`defineUserStats()` ¤

Derived classes add each stat with addUserStat().

`getSpikeValue(spikeIdx, theKey)` ¤

Get a single spike analysis result from key.

Parameters:

Name	Type	Description	Default
`spikeIdx`	`int`	The spike index, 0 based.	required
`theKey`	`str`	Name of the analysis result defined internal name.	required

Raises:

Type	Description
`KeyError`	If theKey is not a key in analysis results.
`IndexError`	If spikeIdx is beyond number of spikes -1.

Source code in sanpy/user_analysis/baseUserAnalysis.py

def getSpikeValue(self, spikeIdx, theKey):
    """Get a single spike analysis result from key.

    Parameters
    ----------
    spikeIdx : int
        The spike index, 0 based.
    theKey : str
        Name of the analysis result defined internal name.

    Raises
    ------
    KeyError
        If theKey is not a key in analysis results.
    IndexError
        If spikeIdx is beyond number of spikes -1.
    """
    try:
        theRet = self.ba.spikeDict[spikeIdx][theKey]
        return theRet
    except KeyError as e:
        logger.error(f'User internal stat does not exist "{theKey}"')
    except IndexError as e:
        logger.error(
            f"spikeIdx {spikeIdx} is out of range, max value is {self.ba.numSpikes}"
        )

`getSweepC()` ¤

Get the DAC axis of a recording.

Source code in sanpy/user_analysis/baseUserAnalysis.py

def getSweepC(self):
    """Get the DAC axis of a recording."""
    return self.ba.fileLoader.sweepC

`getSweepX()` ¤

Get the x-axis of a recording.

Source code in sanpy/user_analysis/baseUserAnalysis.py

def getSweepX(self):
    """Get the x-axis of a recording."""
    return self.ba.fileLoader.sweepX

`getSweepY()` ¤

Get the y-axis of a recording.

Source code in sanpy/user_analysis/baseUserAnalysis.py

def getSweepY(self):
    """Get the y-axis of a recording."""
    return self.ba.fileLoader.sweepY

`run()` ¤

Run user analysis. Calculate values for each new user stat.

Source code in sanpy/user_analysis/baseUserAnalysis.py

def run(self):
    """Run user analysis. Calculate values for each new user stat."""

`setSpikeValue(spikeIdx, theKey, theVal)` ¤

Set the value of a spike key.

Parameters:

Name	Type	Description	Default
`spikeIdx`	`int`	The spike index , 0 based.	required
`theKey`	`str`	Name of the user defined internal name.	required
`theVal`		The value for the key, can be almost any type like (float, int, bool, dict, list)	required

Raises:

Type	Description
`KeyError`	If theKey is not a key in analysis results.
`IndexError`	If spikeIdx is beyond number of spikes -1.

Source code in sanpy/user_analysis/baseUserAnalysis.py

def setSpikeValue(self, spikeIdx, theKey, theVal):
    """Set the value of a spike key.

    Parameters
    ----------
    spikeIdx : int
        The spike index , 0 based.
    theKey : str
        Name of the user defined internal name.
    theVal :
        The value for the key, can be almost any type like
        (float, int, bool, dict, list)

    Raises
    ------
    KeyError
        If theKey is not a key in analysis results.
    IndexError
        If spikeIdx is beyond number of spikes -1.
    """
    try:
        self.ba.spikeDict[spikeIdx][theKey] = theVal
    except (KeyError) as e:
        logger.error(f'User internal stat does not exist "{theKey}"')
    except (IndexError) as e:
        logger.error(
            f"spikeIdx {spikeIdx} is out of range, max value is {self.ba.numSpikes}"
        )

Functions¤

`findUserAnalysisStats()` ¤

Get the stat names of all user defined analysis.

This is determined once at runtime. If files change, sanpy must be restarted.

Source code in sanpy/user_analysis/baseUserAnalysis.py

def findUserAnalysisStats() -> List[dict]:
    """Get the stat names of all user defined analysis.

    This is determined once at runtime. If files change, sanpy must be restarted.
    """
    userStatList: List[dict] = []
    objList = _getObjectList()  # list of dict
    for obj in objList:
        # sanpy._util.pprint(obj)
        # print('')

        # instantiate the object
        userObj = obj["constructor"](ba=None)

        userObjStatDict = userObj._getUserStatDict()

        for k, v in userObjStatDict.items():
            oneUserStatDict = {k: v}
            userStatList.append(oneUserStatDict)

    return userStatList

`runAllUserAnalysis(ba, verbose=False)` ¤

Run all user defined analysis.

Notes¤

Called at end of sanpy.bAnalysis.detect()

Source code in sanpy/user_analysis/baseUserAnalysis.py

def runAllUserAnalysis(ba, verbose=False):
    """Run all user defined analysis.

    Notes
    -----
    Called at end of sanpy.bAnalysis.detect()
    """

    # step through each
    objList = _getObjectList()  # list of dict

    if verbose:
        logger.info(f"objList: {objList}")
    for obj in objList:
        # instantiate and call run (will add values for stats
        # was this
        # userObj = obj(ba)
        # userObj.run()

        try:
            # instantiate a user object
            userObj = obj["constructor"](ba)

            # run the analysis
            userObj.run()  # run the analysis and append to actual ba object
        except Exception as e:
            logger.error(f"Exception in running user defined analysis: {e}")
            logger.error(traceback.format_exc())

baseUserAnalysis

Classes¤