A Python package to analyze flouresence intermittency data of quantum dots
Project description
QuantumBlink
INTRODUCTION
QunatumBlink is a python module developed by Anoop A Nair, under the supervison of Vishnu E K,Ph.D [@ K.G.T. Labs]. It helps in the analysis of flouresence intermittency data obtained from the MT-300 single photon detector. The module when provided with the Intensity vs Time trace derives the ON/OFF event PDFs and the correlations in data indicating the memory effect.
HOW TO INSTALL
The Quantum Blink
module depends on the numpy
module for most of it's functionality.
To Install numpy
use:
pip install numpy
To install QuantumBlink
use:
pip install QuantumBlink
To install QuantumBlink
of a particular version say 1.x use:
pip install QuantumBlink==1.x
HOW TO USE
The module can be imported after installation using:
import QuantumBlink as qb
The csv file should contain two columns the first one being the time and second one being the intesity values.
KEYWORDS and METHODS
> Data Acquisition
>> Intensity data
IntensityData = IntensityDataAcquire(PATH)
1.INPUT
- PATH = "the path to the csv data file" 2.OUTPUT
- IntensityData = array of intesity values
> The ON/OFF Events
>> ON-OFF durations
Positives , Negatives = Power_dist_one(PATH,Threshold,exptime)
1.INPUT
- PATH = "the path to the csv data file".
- Threshold = This specifies the instensity level above which events are treated as positve and below which events are treated as negative.
- exptime = The time interval between each consecutive event. 2.OUTPUT
- Positives = array of ON time durations
- Negatives = array of OFF time durations
>> OFF-time distribution
Pdf_accept_off,Offtime = Offtime_pdf(PATH,Threshold,exptime)
1.INPUT
- PATH = "the path to the csv data file".
- Threshold = This specifies the instensity level above which events are treated as positve and below which events are treated as negative.
- exptime = The time interval between each consecutive event. 2.OUTPUT
- Pdf_accept_off = The probability distribution of OFF-time durations
- Offtime = array of distinct OFF-time durations
>> ON-time distribution
Pdf_accept_on,Ontime = Ontime_pdf(PATH,Threshold,exptime)
1.INPUT
- PATH = "the path to the csv data file".
- Threshold = This specifies the instensity level above which events are treated as positve and below which events are treated as negative.
- exptime = The time interval between each consecutive event. 2.OUTPUT
- Pdf_accept_on = The probability distribution of ON-time durations
- Ontime = array of distinct ON-time durations
> Event Duration info
>> ON time ratio
On_ratio = OnTimeFraction(PATH,Threshold,exptime)
1.INPUT
- PATH = "the path to the csv data file".
- Threshold = This specifies the instensity level above which events are treated as positve and below which events are treated as negative.
- exptime = The time interval between each consecutive event. 2.OUTPUT
- On_ratio = The fraction of ON events.
>> OFF time ratio
Off_ratio = OffTimeFraction(PATH,Threshold,exptime)
1.INPUT
- PATH = "the path to the csv data file".
- Threshold = This specifies the instensity level above which events are treated as positve and below which events are treated as negative.
- exptime = The time interval between each consecutive event. 2.OUTPUT
- Off_ratio = The fraction of OFF events.
>> ON-OFF ratio
ON_OFF_ratio = OnOffRatio(PATH,Threshold,exptime)
1.INPUT
- PATH = "the path to the csv data file".
- Threshold = This specifies the instensity level above which events are treated as positve and below which events are treated as negative.
- exptime = The time interval between each consecutive event. 2.OUTPUT
- ON_OFF_ratio = The ratio of ON to OFF events.
>> OFF-ON ratio
OFF_ON_ratio = OffOnRatio(PATH,Threshold,exptime)
1.INPUT
- PATH = "the path to the csv data file".
- Threshold = This specifies the instensity level above which events are treated as positve and below which events are treated as negative.
- exptime = The time interval between each consecutive event. 2.OUTPUT
- OFF_ON_ratio = The ratio of OFF to ON events.
>> TOTAL ONtime
TOTAL_ONTIME = TotalOnTime(PATH,Threshold,exptime)
1.INPUT
- PATH = "the path to the csv data file".
- Threshold = This specifies the instensity level above which events are treated as positve and below which events are treated as negative.
- exptime = The time interval between each consecutive event. 2.OUTPUT
- TOTAL_ONTIME = The total time occupied by ON events.
>> TOTAL OFFtime
TOTAL_OFFTIME = TotalOffTime(PATH,Threshold,exptime)
1.INPUT
- PATH = "the path to the csv data file".
- Threshold = This specifies the instensity level above which events are treated as positve and below which events are treated as negative.
- exptime = The time interval between each consecutive event. 2.OUTPUT
- TOTAL_OFFTIME = The total time occupied by OFF events.
> Mean, Min, Max intensities
>> The min, max and average intesity of tthe data
AverageIntensity = AverageIntensity(PATH)
1.INPUT
- PATH = "the path to the csv data file". 2.OUTPUT
- AverageIntensity = The Average intensity calculated from the data.
MaxIntensity = MaxIntensity(PATH)
1.INPUT
- PATH = "the path to the csv data file". 2.OUTPUT
- MaxIntensity = The maximum intensity calculated from the data.
MinIntensity = MinIntensity(PATH)
1.INPUT
- PATH = "the path to the csv data file". 2.OUTPUT
- MinIntensity = The minimum intensity calculated from the data.
>> The average intesity between two intensity levels
Intensity_average = AverageIntensityBetween(PATH,Threshold1,Threshold2)
1.INPUT
- PATH = "the path to the csv data file".
- Threshold1 = The upper threshold
- Threshold2 = The lower threshold 2.OUTPUT
- Intensity_average = The average intensity between the upper and lower threshold
> Memory Effect
>> ON-OFF Correlation
XX,YY,R1 = OnOffCorr(PATH,Threshold,exptime)
1.INPUT
- PATH = "the path to the csv data file".
- Threshold = This specifies the instensity level above which events are treated as positve and below which events are treated as negative.
- exptime = The time interval between each consecutive event. 2.OUTPUT
- XX = array of ON/OFF events .
- YY = array of ON/OFF events .
- R1 = The correlation coefficient.
X_x_log,Y_y_log,R1 = OnOffCorrLog(PATH,Threshold,exptime)
1.INPUT
- PATH = "the path to the csv data file".
- Threshold = This specifies the instensity level above which events are treated as positve and below which events are treated as negative.
- exptime = The time interval between each consecutive event. 2.OUTPUT
- X_x_log = array of log value of ON/OFF events .
- Y_y_log = array of log value of ON/OFF events .
- R1 = The correlation coefficient.
>> ON-ON Correlation
XX,YY,R1 OnOnCorr(PATH,Threshold,exptime)
1.INPUT
- PATH = "the path to the csv data file".
- Threshold = This specifies the instensity level above which events are treated as positve and below which events are treated as negative.
- exptime = The time interval between each consecutive event. 2.OUTPUT
- XX = array of ON events .
- YY = array of ON events .
- R1 = The correlation coefficient.
X_x_log,Y_y_log,R1 = OnOnCorrLog(PATH,Threshold,exptime)
1.INPUT
- PATH = "the path to the csv data file".
- Threshold = This specifies the instensity level above which events are treated as positve and below which events are treated as negative.
- exptime = The time interval between each consecutive event. 2.OUTPUT
- X_x_log = array of log value of ON events .
- Y_y_log = array of log value of ON events .
- R1 = The correlation coefficient.
>> OFF-OFF Correlation
XX,YY,R1 = OffOffCorr(PATH,Threshold,exptime)
1.INPUT
- PATH = "the path to the csv data file".
- Threshold = This specifies the instensity level above which events are treated as positve and below which events are treated as negative.
- exptime = The time interval between each consecutive event. 2.OUTPUT
- XX = array of OFF events .
- YY = array of OFF events .
- R1 = The correlation coefficient.
X_x_log,Y_y_log,R1 OffOffCorrLog(PATH,Threshold,exptime)
1.INPUT
- PATH = "the path to the csv data file".
- Threshold = This specifies the instensity level above which events are treated as positve and below which events are treated as negative.
- exptime = The time interval between each consecutive event. 2.OUTPUT
- X_x_log = array of log value of OFF events .
- Y_y_log = array of log value of OFF events .
- R1 = The correlation coefficient. """
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