step-detect's Introduction

step-detect

Python algorithms for autonomous step detection in 1D data. Specifically designed for single molecule force spectroscopy, but applicable to any cases in which there are sudden steps in otherwise semi-stable data.

This module contains functions for transforming raw data into a signal that is suitable for step detection. In basic terms, this amounts to edge-preserving smoothing, though in practice the calculation of these methods is slightly more complex. Once the signal is obtained, a simple thresholding algorithm is applied to determine the positions of steps and their relative magnitudes.

The signal-generating functions follow two distinct methods:

Multiscale product as described by Mallat and Zhong, and as implemented by Sadler and Swami.
The t-statistic method of Carter and Cross.

The usage of this module is demonstrated in the supplied demo IPython notebook, which also provides comparision between the above two methods as well as convolution with a derivative-of-Gaussian wavelet (a simpler but less robust method for step detection).

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step-detect's Issues

Reference issue

The link http://www.dtic.mil/dtic/tr/fulltext/u2/a351960.pdf for the paper of Sadler and Swami is broken.

The proper link is:
https://apps.dtic.mil/sti/pdfs/ADA351960.pdf

Getting step size when indices of detected steps have a length of only 1

ipython notebook does not work?

When I try to run it within Github it thinks for a bit then complains "Sorry, something went wrong. Reload?" I tried downloading and converting to Python (via Juniper) so I can see the usage example and it produces a lengthy error report

D:\xxx\Documents\python\Step detect>ipython nbconvert --to=python step_detect_demo.ipynb [TerminalIPythonApp] WARNING | Subcommand ipython nbconvertis deprecated and will be removed in future versions. [TerminalIPythonApp] WARNING | You likely want to usejupyter nbconvert` in the future
[NbConvertApp] Converting notebook step_detect_demo.ipynb to python
Traceback (most recent call last):
File "C:\Anaconda2\Scripts\ipython-script.py", line 10, in
sys.exit(start_ipython())
File "C:\Anaconda2\lib\site-packages\IPython_init_.py", line 119, in start_ipython
return launch_new_instance(argv=argv, **kwargs)
File "C:\Anaconda2\lib\site-packages\traitlets\config\application.py", line 658, in launch_instance
app.start()
File "C:\Anaconda2\lib\site-packages\IPython\terminal\ipapp.py", line 351, in start
return self.subapp.start()
File "C:\Anaconda2\lib\site-packages\nbconvert\nbconvertapp.py", line 337, in start
self.convert_notebooks()
File "C:\Anaconda2\lib\site-packages\nbconvert\nbconvertapp.py", line 507, in convert_notebooks
self.convert_single_notebook(notebook_filename)
File "C:\Anaconda2\lib\site-packages\nbconvert\nbconvertapp.py", line 478, in convert_single_notebook
output, resources = self.export_single_notebook(notebook_filename, resources, input_buffer=input_buffer)
File "C:\Anaconda2\lib\site-packages\nbconvert\nbconvertapp.py", line 407, in export_single_notebook
output, resources = self.exporter.from_filename(notebook_filename, resources=resources)
File "C:\Anaconda2\lib\site-packages\nbconvert\exporters\exporter.py", line 178, in from_filename
return self.from_file(f, resources=resources, **kw)
File "C:\Anaconda2\lib\site-packages\nbconvert\exporters\exporter.py", line 196, in from_file
return self.from_notebook_node(nbformat.read(file_stream, as_version=4), resources=resources, **kw)
File "C:\Anaconda2\lib\site-packages\nbformat_init_.py", line 141, in read
return reads(fp.read(), as_version, **kwargs)
File "C:\Anaconda2\lib\site-packages\nbformat_init_.py", line 74, in reads
nb = reader.reads(s, **kwargs)
File "C:\Anaconda2\lib\site-packages\nbformat\reader.py", line 58, in reads
nb_dict = parse_json(s, **kwargs)
File "C:\Anaconda2\lib\site-packages\nbformat\reader.py", line 17, in parse_json
raise NotJSONError(("Notebook does not appear to be JSON: %r" % s)[:77] + "...")
NotJSONError: Notebook does not appear to be JSON: u'\n\n\n\n\n\n\n<html lan...

If you suspect this is an IPython bug, please report it at:
https://github.com/ipython/ipython/issues
or send an email to the mailing list at [email protected]

You can print a more detailed traceback right now with "%tb", or use "%debug"
to interactively debug it.

Extra-detailed tracebacks for bug-reporting purposes can be enabled via:
c.Application.verbose_crash=True`

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