Commit cf0ab135 authored by Gregor Moenke's avatar Gregor Moenke

Merge branch 'master' into 'develop'

README update

See merge request !34
parents 3dfe05db c30ba177
## pyBOAT - A Biological Oscillations Analysis Toolkit ##
[![PyPI version](https://badge.fury.io/py/pyboat.svg)](https://badge.fury.io/py/pyboat)
Tools for time-frequency analysis of noisy time series. The
accompanying manuscript "Optimal time frequency analysis for biological data - pyBOAT"
can be found [here](https://biorxiv.org/cgi/content/short/2020.04.29.067744v2).
can be found [here](https://biorxiv.org/cgi/content/short/2020.04.29.067744v3).
Questions, comments etc. please to <gregor.moenke@embl.de>.
### Features ###
......@@ -41,6 +42,12 @@ is also a Navigator App, it will now (along with other apps) show up in the main
Finally hitting ```Install``` will download and install pyBOAT. Thereafter,
pyBOAT can be started by simply clicking on ```Launch``` inside the Navigator.
#### Updates
In case you see a little blue arrow next to the version number, this means
an update is available. Clicking on that cogwheel icon in the upper right corner
allows to run the update and install the latest version of pyBOAT.
#### Installation with Anaconda on the commandline ####
For this, the download and installation of [miniconda](https://docs.conda.io/en/latest/miniconda.html)
......@@ -76,19 +83,25 @@ into the command line.
For running directly from the source, see also [this document](./doc/gui_from_source.md)
### Usage ###
## Usage ##
-------------
#### Data import ####
Almost every input field and checkbox has a tool tip attached for quick reference.
Just open your saved time-series data by using ``` Open ```
### Data import ###
In general pyBOAT expects tabular data, with each column
representing a signal. Just open your saved time-series data by using ``` Open ```
from the (small) main window. Supported input formats are:
``` .xls, .xlsx, .csv, .tsv``` and ```.txt ```. For other file
extensions, white space separation of the data is assumed.
Please see examples of the supported formats in the
``` example_data ``` directory of this repository.
#### Analysis ####
In case you want to interpolate missing data or you want to define your own
separator, the ```Import..``` button will spawn a menu with further options.
### Analysis ###
After successful import, you can simply click on the table representing
your data to select a specific time-series in the ``` DataViewer ```.
......@@ -99,7 +112,7 @@ The general layout of the ```DataViewer``` to set up the analysis is shown here:
<img src="./doc/DataViewer.png" alt="drawing" width="800"/>
##### Detrending #####
#### Detrending ####
The featured sinc-detrending is an optimal high-pass filter and removes low frequencies (high periods)
......@@ -109,7 +122,7 @@ Check the ``` Trend ``` and/or ``` Detrended Signal ``` checkbox(es)
and click ``` Refresh Plot ```
to see the effect of the filter on the selected time series.
##### Amplitude Envelope #####
#### Amplitude Envelope ####
If there is a strong trend in the amplitudes alone, for example a slow decay, pyBOAT offers
a simple sliding-window operation to estimate this envelope. The ```Window Size```
......@@ -119,7 +132,7 @@ to see the detected envelope. When running the
Wavelet analysis, there is an option ```Normalize with Envelope``` to remove it
from the signal.
##### Set up Wavelet Analysis #####
#### Setting up the Wavelet Analysis ####
Set the parameters for the Wavelet Analysis in the lower right:
......@@ -133,7 +146,7 @@ Set the parameters for the Wavelet Analysis in the lower right:
Leave the ``` Use the detrended signal ``` box checked if you want to use the sinc-detrending.
``` Analyze Signal ``` will perform the Wavelet transform of the selected signal.
#### Wavelet Power Spectrum ####
### Wavelet Power Spectrum ###
The input signal for the Wavelet analysis and the resulting 2d-power-spectrum are shown with aligned time axis.
The y-axis indicates the periods(frequencies) selected for analysis.
......@@ -148,7 +161,7 @@ respective box.
<img src="./doc/spectrum.png" alt="drawing" width="500"/>
##### Ridge Analysis #####
#### Ridge Analysis ####
To extract intantaneous frequency and associated phase, a 1d-*ridge* (a profile) has to be traced through the
2d-power spectrum:
......@@ -169,7 +182,7 @@ red line in spectrum plot, note that no default ridge is shown in a fresh
``` Wavelet Spectrum ``` window. For a quick check hit the ``` Detect Maximum Ridge ``` button.
You can also smooth the ridge if needed.
##### Ridge Results #####
### Ridge Results ###
......
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