UConnRCMPy 3.0.5

A package to process RCM data

UConnRCMPy

Data processing code for the RCM at UConn. See the license file for information about the license for this code.

CI Status

Travis: AppVeyor: Codecov:

DOI

Change Log

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

Unreleased

Added

Fixed

Changed

Removed

[3.0.5] - 2017-06-21

Fixed

• Exception no longer raised when the EOC time is changed of an experiment that was mischaracterized as non-reactive

3.0.4 - 2017-06-21

Fixed

• EOC time not respected after it had been changed in change_EOC_time

3.0.3 - 2017-06-16

Added

• Function to manually set the EOC time, change_EOC_time

Fixed

• Comparing T_EOC between reactive and non-reactive caused a ValueError

• Add copy argument to AltExperiment class initializer

• Fix how adding cases is handled in AltCondition

Changed

Removed

3.0.2 - 2017-04-19

Added

• CITATION file

• PyPI packages

Fixed

• Deploy doctr to the root directory (see drdoctr/doctr#157 and drdoctr/doctr#160)

Changed

• DOI badges point to latest DOI from Zenodo

• Relicensed to BSD 3-Clause

3.0.1 - 2017-02-21

Added

• Copy keyword in Experiment init to avoid auto-copy to clipboard

• Regression tests for Experiment, including ignition delay, p_EOC, and T_EOC estimate

• kwargs are passed through to the Experiment init in add_experiment

Fixed

• copy=False kwarg passed to add_experiment in tests fixes tests on Travis

• Load CTI file instead of from source string to avoid Cantera/cantera#416

Changed

• Butterworth filter is now first order

• Butterworth filter cutoff frequency is no longer corrected

• End point for linear fit of filter residuals is chosen automatically

• Derivative is smoothed with moving average

3.0.0 - 2017-02-07

Added

• Print warning when the simulated TCs don’t match

• Python 3.6 builds on Travis

• Conda builds on Travis/Appveyor upload to anaconda.org when a tag is pushed.

• Appveyor builds for Windows tests/packaging

• Prompt user for filter frequency when auto-setting fails

• Label for raw pressure line

• Refactor Simulation class to new module

• Conda recipe

• Summary output from Condition

• String input to Experiment

• Add types to the docs for constants

• __repr__ for all classes

• Text-file output from relevant trace-type classes

• reactive_file is an attribute of Condition as a property

• This CHANGELOG file

• Automatic filter cutoff frequency selection and override functions

• Upload docs to gh-pages with doctr

• Disable Cantera thermo warnings after loading a CTI file for the first time

• volume-trace.yaml file is automatically written

• Version information is stored in _version.py

Fixed

• Travis builds now fail appropriately

• Added MANIFEST.in and modified setup.py to include test data files

• Replot lines when filtering frequency is changed

• Fix docs after dataprocessing -> conditions/experiments module split

• Unsuppress thermo warnings before loading a new CTI file

• Properly set reactive_case and nonreactive_case, and other attributes important for the VolumeTrace generation

• Filter frequency has to be set after the experiment sampling frequency is calculated

• Writing the volume-trace.yaml file now has filenames instead of Path reprs

• Time in figure legend has a colon

Changed

• Catch FileNotFoundErrors instead of OSErrors when files are missing

• Raise exceptions if CTI arguments are specified incorrectly to Experiment

• Convert all time axes on figures to ms

• Split the dataprocessing module into experiments and conditions modules

• Use slices to compute the derivative of the experimental pressure trace

• A CTI filename is required as input when Condition is instantiated

• The creation of the volume trace is controlled by instance attributes rather than volume-trace.yaml

• Minimum version of Cantera is 2.3.0

Removed

• CanSen dependency is no longer required

• Voltage traces are no longer smoothed, and the smoothing function has been removed

2.1.0 - 2016-05-31

Added

• Docs for dataprocessing

• Matplotlib to intersphinx

• Alternate class for processing experimental data AltExperiment

• The year is stored in the experiment_parameters dictionary

• Plot the P0 fit line on nonreactive plots

• Axis labels on figures

Fixed

• Default documentation role is py:obj

• Import from experiment module should be dataprocessing module

• Wrong version in docs

• Get the non-reactive experiment to plot in create_volume_trace

• The zeroed time and pressure trace should come from the pressure_trace instance in process_folder

• Include offset in pressure trace timing calculations

• Documentation typos in filtering function and finding PC

• Using a float as an index to a NumPy array is deprecated, so don’t do that

Changed

• Use online Cantera docs for intersphinx

• The exception generated if calculation of TC fails is printed

• parse_file_name is a method of Experiment

• Reduce the search increment for finding PC from 100 to 50

Removed

• PressureFromVolume and VolumeFromPressure state can no longer be set by P and v

2.0.2 - 2016-01-24

Added

• Condition is imported in __init__.py

2.0.1 - 2016-01-23

Fixed

• Wrong figure name used in compare_to_sim

• Derivative of simulated pressure trace was computed incorrectly

Changed

• Only get the parameters needed from the YAML file, instead of loading the whole thing every time

• Simulations are plotted with the time-axis in ms and with the zero at EOC

2.0.0 - 2016-01-23

Added

• Sphinx documentation

Fixed

• Clipboard pasting works on OS X and Windows

Changed

• Refactor most functionality into classes

• Remove ParsedFilename class

• Remove old, unused, modules including nonreactive.py, volume_trace.py, and experiments.py->``dataprocessing.py``

• Set the overall and first stage ignition delays, and the TC of nonreactive experiments to 0

1.0.7 - 2016-12-01

Added

• Low-pass filtering function for the voltage signal

• First stage ignition delay is automatically calculated

Fixed

• Errors in computing the temperature are caught now, instead of crashing the analysis

• Eliminate deprecation warning about ReactorNet.step() by checking the version of Cantera being used

Changed

• Change offset for ignition delay calculation from 5 ms to 2 ms

• Use FFT convolve from scipy instead of convolve from numpy because the FFT was 100x faster

• The voltage is low-pass filtered and then moving-average smoothed, rather than just being smoothed

• Increase the smoothing window for the derivative from 5 to 151

• The compression time from the YAML file is used as the end time when fitting the initial period of the pressure trace

1.0.6 - 2015-07-18

Added

• Option to specify end_time or end_temp to the simulation in the class constructor

1.0.5 - 2015-07-16

Added

• Option to plot results in the ign_loop script

1.0.4 - 2015-07-16

Fixed

• Bugs related to missing pathlib imports in traces files

1.0.3 - 2015-07-16

Added

• New dependency on the pathlib module, requiring Python >= 3.4

Fixed

• The path to search for files to process in ign_loop is computed at runtime rather than import-time

• Fix typo in ParsedFilename docs

1.0.2 - 2015-07-16

Fixed

• Ignore the build directory

Changed

• Rename class PressureTrace to ExperimentalPressureTrace

• The smoothing function sets the first (span-1)/2 data points equal to the value there

• Refactor voltage variable name to be signal

• Smooth the voltage first, then compute the pressure, rather than the other way around

1.0.1 - 2015-07-16

Added

• Filename for the reactive experiment is loaded from the volume-trace.yaml file

Fixed

• Minimize code inside with-statement for YAML file

• Ignore dist folder from Git

Changed

• The name of the script to run an analysis of a folder is changed from process-ignition-loop to ignloop

1.0.0 - 2015-06-28

Added

• Basic functionality of class-based interface to process data

Citation of UConnRCMPy

To cite UConnRCMPy in a scholarly article, please use

B. W. Weber, R. Fang, and C.J. Sung. (2017) UConnRCMPy v3.0.2 [software]. Zenodo. https://doi.org/10.5281/zenodo.594918

A BibTeX entry for LaTeX users is

@software{uconnrcmpy,
  title = {{{UConnRCMPy}}},
  url = {https://github.com/bryanwweber/UConnRCMPy},
  version = {3.0.3},
  author = {Weber, Bryan William and Fang, Ruozhou and Sung, Chih-Jen},
  date = {2017-04},
  doi = {10.5281/zenodo.594918}
}

The DOI for the latest version can be found in the badge at the top. If you would like to cite a specific, older version, the DOIs for each release are:

• v3.0.4: 10.5281/zenodo.815568

• v3.0.3: 10.5281/zenodo.810181

• v3.0.2: 10.5281/zenodo.556469

• v3.0.1: 10.5281/zenodo.321427

• v3.0.0: 10.5281/zenodo.269678