Visualization Tools

Python based visualization tools for low dimensional embeddings of spectral and neural data

Spectrogram Viewer

Quick tool for visual comparison of two 'Wav' files

Dependencies: matplotlib, pyqtgraph, PyQt5, scipy, numpy

Run viewer.py or import DataPlotter class and run the following commands

plotter = DataPlotter()
plotter.setupPlot()
plotter.addFile('/Users/ethanmuchnik/Desktop/specViewer/Demo_Wav/USA5207_45107.22309894_6_30_6_11_49.wav','top')
plotter.addFile('/Users/ethanmuchnik/Desktop/specViewer/Demo_Wav/USA5207_45107.22652648_6_30_6_17_32.wav','bottom')
plotter.startLink()
plotter.show()

Neural Embedding Scroller

Traverse neural, behavioral, and low dimensional data Dependencies:: matplotlib, pyqtgraph, PyQt5, numpy

Run improvedGUI.py or import DataPlotter class and run the following commands

# Instantiate the plotter    
plotter = DataPlotter()

# Accept folder of data
plotter.accept_folder('/Users/ethanmuchnik/Desktop/Series_GUI/SortedResults/Pk146-Jul28')

# Show
plotter.show()

Audio Embedding Selection Tool

Dependencies:: matplotlib, pyqtgraph, PyQt5, numpy

Inputs:

npz file with:

• 'embVals' : N by 2 array of x,y values for low dimensional embedding
• 'embStartEnd' : 2 by N array of start,end times for each of the N slices
• 'behavioralArr': Np array of spectrogram (must be representative of the time bounded by the first start and last end of embStartEnd)

app = QApplication([])
# Instantiate the plotter    
plotter = DataPlotter()
# Accept file of data
plotter.plot_file('/Users/ethanmuchnik/Downloads/demoCanaryLarge3.npz')
plotter.addROI()
# Show
plotter.show()

Plotting Techniques/Ideas

Pixelated UMAP

PYTHON NOTEBOOKS

See the IPYNB notebooks in the corresponding folder. To see descriptions follow the link:

https://docs.google.com/document/d/1b8mM1iIZQ_d6nVThbMlvDFKTJ4s32-cboXrCIKfY-aQ/edit?usp=sharing

Contact

• Ethan Muchnik (Gardner Lab)
• [email protected]