A toolbox to analyse diagnostic data!
Diagnostics is a Python module designed to make analysis of diagnostic data easier. It comes with a couple of clear data-structures with automatic quality checks, easy Boolean logic operators and built-in bookkeeping. To top that off, it’s built on numpy!
The diagnostics library is tested on python 3.7. However, it should run on python 3.6 and 3.5 as well.
You can install the library using pip:
pip install pydiagnostics
Alternatively, you can clone the repository and use setup.py to install:
git clone https://github.com/tim00w/diagnostics.git cd diagnostics python setup.py install
This project strives to abide by generally accepted best practices in open-source software development:
The docs are hosted on ReadTheDocs.
Eager to begin and no time to read the documentation? Here is a quickstart!
Diagnostic events are derived from from real occurances. For instance, your phone will probably generate a message (event) if your battery is running low (percentage below threshold value). The diagnostics library has a TimeSerie class that can capture these occurances.
For example, a TimeSerie representing your battery life, which drains 0.01% each second:
import numpy as np import diagnostics as ds battery_life = ds.TimeSerie(np.arange(100, 0, -0.01), fs=1)
the first argument is consists of a data array (both list() and numpy.array() are supported), and additionally you can provide some keyword parameters. Here we’ve provided the sample frequency (fs) which is 1 Hz, because we said our battery drains 0.01% each second. In this particular case we could’ve left fs out, since the default value of fs is also 1.
Now that we’ve got our data, we can easily visualize this:
There are other keyword parameters that we can use as well, such as t0 (start time of TimeSerie in posixtime or a datetime object), and a name (default is an empty string).
from datetime import datetime battery_life = ds.TimeSerie(np.arange(100, 0, -0.01), fs=1, t0=datetime(2019,1,1,8,5), # 2019-01-01 08:05 name='battery life')
Now we’ve got our battery life set to a specific (start-)datetime, and gave it a name. Both will come in handy later.
Let’s be honest, the battery percentage of your phone does not really matter to you, unless it goes below a certain threshold. Luckily for us, our TimeSerie can easily be converted to a BooleanTimeSerie, which only contains boolean values of when the percentage reaches below 25%:
battery_below25 = battery_life <= 25 battery_below25.plot(show=True)
Now that’s easy! We can see that our battery goes below 25% at HH:MM:SS.
You could argue that our BooleanTimeSerie contains a lot of data points with the same value. I’d agree with you, and therefore introduce a class that only keeps track of the changes in data points, the StateChangeArray:
battery_low_state = battery_below25.to_statechangearray()
Alternatively, we can create a StateChangeArray (or BooleanStateChangeArray, you can probably guess the difference :smile:) from scratch:
s = ds.StateChangeArray([1, 4, 8, 13], t=[1,2,4,8], name='my state') b = ds.BooleanStateChangeArray([True, False, True, False], t=[1,3,6,9], name='b')
Both the data array as the values for time (t) can be list() or np.array(). The time is considered as posixtime. For now it is not possible to give a datetimearray or list of datetimes as an input, but this wil be implemented in the near future.
Comparing TimeSeries and StateChangeArrays
There are more classes besides TimeSeries and StateChangearrays, each with their own advantages and disadvantages. The power of this module lies in clear transformations from one class to another (we’ve already shown the TimeSerie.to_statechangearray() method), and the comparison of multiple classes.
To start with TimeSeries, if two (or more) have the same array_length, t0 and fs, we can easily do calculations with them!
# create two TimeSerie objects that we'll combine a = ds.TimeSerie(np.sin(np.linspace(0, 2*np.pi, 100)), t0=0, fs=1, name='a') b = ds.TimeSerie(np.sin(2* np.linspace(0, 2*np.pi, 100)), t0=0, fs=1, name='b') # It's this easy! c = a + b # We're interested in the more extreme values, lets create TimeSeries for these: d = c <= -1 e = c >= 1 # we'll name them to keep our bookkeeping up to date d.name = 'c <= -1' e.name = 'c >= 1' # and find when one of the above conditions is True! f = d | e # when performing boolean operators ('~', '^', '&', '|'), the library # does it's own bookkeeping: print(f.name) f.plot(show=True)
Comparing StateChangeArrays would normally be a bit tricky, since the data is most likely non-linearly spaced. This means that we can’t just perform vectorized boolean operations, but we’ll need to combine both data values as well as their respective points in time.
Luckily for us, the StateChangeArray has this built in:
a = StateChangeArray([True, False, True, False], t=[2,4,6,8], name='a') b = StateChangeArray([True, False, True, False], t=[3,5,7,9], name='b') c = a | b d = a & b e = ~a f = a ^ a g = a ^ e
That’s pretty great right?
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