FastAnalysis

FastAnalysis is a python module for analysing result from FastTrack tracking software.

Project info

Installation

To install the module:

From PyPi

pip install fastanalysis

From source

git clone https://github.com/FastTrackOrg/FastAnalysis.git
cd FastAnalysis
pip install .

Development

The project is under active development and do not have public API documentation, a more or less complete API documentation can be generated using Sphinx.

Documentation

Retrieve data from a tracking.txt file

A tracking.txt file can be loaded and several method are available to select objects and frames:

import fastanalysis as fa

tracking = fa.Load("tracking.txt")
fa.isObjectsInFrame(0, 100) # Check if object with id 0 is in the 100th frame
fa.isObjectsInFrame([0, 1], 100) # Check if object with id 0 and 1 is in the 100th frame
a = tracking.getObjectsInFrames(0, 100) # Select data of the object with id 0 in the 100th frame
b = tracking.getObjectsInFrames([0,1], [100,101]) # Select data of the object with id 0 and 1 in the 100th and 101th frames
c = tracking.getObjects(0) # Select data of the object with id 0 for all the frames
d = tracking.getObjects([0,1]) # Select data of the object with id 0 and 1 for all the frames
e = tracking.getFrame(100) # Select data for all the objects in the 100th frame
f = tracking.getFrame([100,101]) # Select data for all the objects in the 100th and 101th frames

Export data

import fastanalysis as fa

tracking = fa.Load("tracking.txt")
keys = fa.keys() # List export features
fa.export("output.xlsx", delimiter='\t', keys=["xHead", "yHead", "imageNumber", "id"], ids=None, indexes=None, format="excel") # Export a list of features for all the frames and all the objects in an excel file.
fa.export("output.txt", delimiter='\t', keys=None, ids=None, indexes=None, format="excel") # Export all thefeatures for all the frames and all the objects in an csv file.

Two format are supported: csv and excel.

Plot metrics

import fastanalysis as fa
import matplotlib.pyplot as plt

tracking = fa.Load("tracking.txt")
plotObj = fa.Plot(tracking)
plotObj.velocityDistribution(ids=[0, 1], key="Body", pooled=False, subplots=True) # Plot velocity distribution for objects 1 and 0 in 2 subplots
plotObj.velocityDistribution(ids=[0, 1], key="Body", pooled=False, subplots=False) # Plot velocity distribution for objects 1 and 0 in 1 plot
plotObj.velocityDistribution(ids=[0, 1], key="Body", pooled=True) # Plot velocity distribution for objects 1 and 0 pooled in 1 distribution