Detector Data Processing Package
Project description
detprocess: Detector processing code for feature extraction
detprocess is a Python package meant for feature extraction from raw detector data saved by pytesdaq. The main functionality of the code is contained in detprocess.process, which contains all the possible features to be extracted and the general pipeline of how features are extracted. This package also contains helper IO functions for loading events from pytesdaq and saving the processed data as Pandas DataFrames.
Table of Contents
Installation
To install the most recent release of detprocess, type the following line into your command line
pip install detprocess --upgrade
To install the most recent development version of detprocess, clone this repo, then from the top-level directory of the repo, type the following line into your command line
pip install .
If using a shared Python installation, you may want to add the --user flag to the above line. Note the package requirements, especially the need for QETpy and pytesdaq.
Usage
One of the goals of this package is to keep the feature extraction pipeline simple and modular. The pipeline in mind can be approximated as follows:
- Know what features you want to extract, see: Available Features
- Create a YAML file specifying feature extraction options, see: YAML File
- Run the feature extraction code on your data, see: Extracting Features
- Analyze the features that you have extracted, see: Loading Features
Available Features
The available features to extract are stored as the static methods of detprocess.SingleChannelExtractors. Each of these methods take your data and extract that specific feature from each event. At this time, the available features are:
of_nodelay: returns the no delay optimum filter amplitude and chi-square (as in, the amplitude if the template is not allowed a time degree-of-freedom)of_unconstrained: returns the unconstrained optimum filter amplitude, time offset, and chi-squareof_constrained: returns the constrained optimum filter amplitude, time offset, and chi-square, where a window constraint is specifiedbaseline: returns the average value from the beginning of an event up to some specified indexintegral: returns the integral of the event (no baseline subtraction) from some specified start index to some specified end indexmaximum: returns the maximum value of the event from some specified start index to some specified end indexminimum: returns the minimum value of the event from some specified start index to some specified end indexenergyabsorbed: returns the energy absorbed by a Transition-Edge Sensor (TES) based on the inputted parameters that correspond to the TES bias point
More features can be added either locally, or if there is a feature that is universally useful, then please submit a Pull Request! See Advanced Usage for instructions on adding features.
There are also features that are stored directly in pytesdaq files, which detprocess will also extract. These are:
eventnumbereventindexdumpnumberseriesnumbereventtimetriggertypetriggeramptriggertime
To understand these more, we direct the user to pytesdaq's Documentation.
YAML File
The YAML file contains nearly all of the information needed to extract features from your data. This is done on purpose, as it allows the user to easily reuse/change their YAML files for different processing, to easily version control their processing, and easily share their processing setup with collaborators. To make sure we can do this, the YAML must have a specific format. Here's an example below.
detector1:
template_path: /path/to/template.txt
psd_path: /path/to/psd.txt
of_nodelay:
run: True
of_unconstrained:
run: False
of_constrained:
run: False
windowcenter: 0
nconstrain: 100
baseline:
run: True
end_index: 16000
integral:
run: True
start_index: 0
end_index: 16000
In this YAML file, we first specify which channel will be processed, in this case detector1. This should match the channel name in the corresponding pytesdaq file. We have supplied absolute paths to both the pulse template and the current-referenced power spectral density (PSD) to be used by the optimum filters. The pulse template should be a single array that contains the expected pulse shape, normalized to have a pulse amplitude of 1 and have a baseline of 0. The current-referenced PSD should be a single array that contains the two-sided PSD in units of $\mathrm{A}^2/\mathrm{Hz}$. Note that both of these will should have the same digitization rate and/or length as the data that will be processed to be able to calculate the optimum filter features.
We have also specified to extract 3 different features from each event: of_nodelay, baseline, and integral. This is done by specifying run: True in the file, as compared to run: False for of_unconstrained and of_constrained. Note that it is fine to simple exclude features from the YAML file, as they simply will not be calculated (e.g. energyabsorbed is not included in this example).
For the features themselves, the functions to extract them may require extra arguments. In this example, baseline requires the user to pass the end_index value, and integral requires the user to pass both start_index and end_index. There are no default values for these features, so these arguments must be passed. To know what is needed for each feature, the docstrings of these features can be accessed through detprocess.SingleChannelExtractors.
Extracting Features
Feature extraction is meant to be very easy once we have our features and our YAML file. Essentially all of the work is done by detprocess.process_data. This function takes the absolute path to the file to be processed and the absolute path to the YAML file, and then will return a DataFrame containing all of the extracted features. The user can ensure these are automatically saved to a folder of their choice by also passing a path to the savepath optional argument. An example of the expected workflow is shown in examples/run_detprocess.ipynb.
Loading Features
After feature extraction is complete (assuming that the user chose to save the processed data), it is simple to load the features. As part of the IO functionality, detprocess has a function to load the extracted features into a Pandas DataFrame. This is done by detprocess.io.load_features, the example notebook examples/run_detprocess.ipynb shows usage of this function.
After loading features, detprocess includes many helpful core functions for applying data quality cuts, plotting features, and doing maximum likelihood fits of energy spectra. We have also written an example notebook for using the maximum likelihood fitting routines: examples/max_likelihood.ipynb.
Advanced Usage
Beyond the basic functionality of detprocess, advanced users may want to do more, such as adding new default features, fast development of new features, or interfacing with a high-performance computing (HPC) cluster. In this section, we detail how to do these.
Adding New Default Features
For advanced users, there may be a need to add new default features for extraction which are not currently included (see Developing Features for more on one-off or fast development of features). To do this, the user must add a new feature as a staticmethod in detprocess.SingleChannelExtractors. To understand how to do this, let's look at a couple of the currently-supported features. Below we show an excerpt of the feature definitions, showing how of_nodelay and integral are defined in detprocess/process/_features.py.
class SingleChannelExtractors(object):
"""
A class that contains all of the possible feature extractors
for a given trace, assuming processing on a single channel.
Each feature extraction function is a staticmethod for processing
convenience.
"""
@staticmethod
def of_nodelay(trace, template, psd, fs, **kwargs):
"""
Feature extraction for the no delay Optimum Filter.
Parameters
----------
trace : ndarray
An ndarray containing the raw data to extract the feature from.
template : ndarray
The template to use for the optimum filter.
psd : ndarray
The PSD to use for the optimum filter.
fs : float
The digitization rate of the data in trace.
Returns
-------
retdict : dict
Dictionary containing the various extracted features.
"""
OF = qp.OptimumFilter(
trace,
template,
psd,
fs,
)
ofamp_nodelay, ofchi2_nodelay = OF.ofamp_nodelay()
retdict = {
'ofamp_nodelay': ofamp_nodelay,
'ofchi2_nodelay': ofchi2_nodelay,
}
return retdict
## features between these have been truncated from the source code
@staticmethod
def integral(trace, start_index, end_index, fs, **kwargs):
"""
Feature extraction for the pulse integral.
Parameters
----------
trace : ndarray
An ndarray containing the raw data to extract the feature from.
start_index : int
The index of the trace to start the integration.
end_index : int
The index of the trace to end the integration.
fs : float
The digitization rate of the data in trace.
Returns
-------
retdict : dict
Dictionary containing the various extracted features.
"""
integral = np.trapz(trace[start_index:end_index]) / fs
retdict = {
'integral': integral,
}
return retdict
We should note that, when comparing to our example YAML file, there are three special arguments that are being passed to the features, which we did not directly define in that file: template, psd, and fs. The reason is that template and psd are defined from opening the text files template_path and psd_path, while fs is contained in the pytesdaq file being processed, so it does not need to be defined by the user. These special arguments can always be included in a new feature by directly specifying them, otherwise they are ignored. To support these special features, each extraction function must have **kwargs in its definition.
For the integral feature, we see that there are two arguments which are defined in our example YAML file: start_index and end_index. As these are arguments that are needed specifically for this feature, they must be defined in the YAML file.
Each feature function can return multiple values, if needed, as shown by of_nodelay. The detprocess processing routine will use the defined keys in the returned dictionary retdict to save them to the outputted Pandas DataFrame. Note that, to ensure unique names if we are processing multiple channels in the same file, detprocess will append the channel name to the saved feature. That is, the outputted DataFrame for our example YAML file for these two specified feature function would have the following keys saved: ofamp_nodelay_detector1, ofchi2_nodelay_detector1, and integral_detector1.
To create a new feature, we would follow the format of the above features. Let's create a feature called example_feature, defined below, where some_function takes the place of the code that would be used to extract the features. Let's say this feature needs the parameters param1 and param2, as well as the special argument fs. We include the required **kwargs for support of the special features.
@staticmethod
def example_feature(trace, param1, param2, fs, **kwargs):
"""
Feature extraction for some example feature.
Parameters
----------
trace : ndarray
An ndarray containing the raw data to extract the feature from.
param1 : float
The first parameter to pass to our feature extraction.
param2 : float
The first parameter to pass to our feature extraction.
fs : float
The digitization rate of the data in trace.
Returns
-------
retdict : dict
Dictionary containing the various extracted features.
"""
output1, output2 = some_function(trace, param1, param2, fs)
retdict = {
'example_feature1': output1,
'example_feature2': output2,
}
return retdict
This feature must be added as one of the static methods in the class SingleChannelExtractors, located in detprocess/process/_features.py. After adding the code, the user must then recompile the package via pip install ., and the feature can be extracted by detprocess.
If we added this feature to our example YAML file, the corresponding entry should be of the form (where we are currently passing dummy values to the dummy parameters):
example_feature:
run: True
param1: 0
param2: 1
When running detprocess.process_data, the outputted Pandas DataFrame would then have the keys example_feature1_detector1 and example_feature2_detector1, which can then be accessed by the user in their analysis.
Developing Features
When developing new features or creating one-off features for a specific dataset, it can be inefficient to need to rebuild the package each time a feature is changed. In this scenario, the detprocess.process_data function has a keyword argument called external_file. The user can pass the path to a custom version of the detprocess/process/_features.py file, where the same formatting must be followed (i.e. the functions must be added to a class called SingleChannelExtractors). Below, we show an example of such a file.
import numpy as np
class SingleChannelExtractors(object):
"""
A class that contains all of the possible feature extractors
for a given trace, assuming processing on a single channel.
Each feature extraction function is a staticmethod for processing
convenience.
"""
@staticmethod
def example_feature(trace, param1, param2, fs, **kwargs):
"""
Feature extraction for some example feature.
Parameters
----------
trace : ndarray
An ndarray containing the raw data to extract the feature from.
param1 : float
The first parameter to pass to our feature extraction.
param2 : float
The first parameter to pass to our feature extraction.
fs : float
The digitization rate of the data in trace.
Returns
-------
retdict : dict
Dictionary containing the various extracted features.
"""
output1, output2 = some_function(trace, param1, param2, fs)
retdict = {
'example_feature1': output1,
'example_feature2': output2,
}
return retdict
This is simply using the example_feature feature from the previous section on Adding New Default Features. When using detprocess.process_data, we would simply pass the location of this file to external_file. The processing code would then ignore the default features to extract, and use the features in this example file instead. Note that this means that none of the default features will be calculated, so if those are desired, they should be included in this file being passed to external_file.
The corresponding YAML file should then have the below form, where only this example_feature should be calculated, as it is the only feature in the external file.
detector1:
template_path: /path/to/template.txt
psd_path: /path/to/psd.txt
example_feature:
run: True
param1: 0
param2: 1
Note that, because the OF is so ubiquitous in our processing, detprocess still asks for a template and a psd. This is because every time we carry out feature extraction with data from a detector, the OF will almost certainly be calculated to extract OF amplitudes.
After a feature has been developed, and it seems to be a useful features for general analyses, then it should be added to the default features for this package, which can be done by following the steps in Adding New Default Features.
High-Performance Computing
Detailing this usage is a work-in-progress.
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