getY: Read in Y matrix for SCALPEL.
In scalpel: Processes Calcium Imaging Data

Description Usage Arguments Value Examples

This step allows the user to read in Y, the matrix of raw or processed video data, to use with several plotting functions.

1	getY(scalpelOutput, videoType = "processed", part = NULL)

`scalpelOutput`	An object returned by one of the SCALPEL functions: `scalpel`, `scalpelStep0`, `scalpelStep1`, `scalpelStep2`, or `scalpelStep3`.
`videoType`	Specify whether to read in the processed data from Step 0 (default; `videoType="processed"`) or raw data (`videoType="raw"`).
`part`	The part of the video to read in, if it is split across multiple files. The default is NULL, which means that all parts will be read in and combined.

An object of class scalpelY that can be provided as the Y argument in plotFrame, plotVideoVariance, plotBrightest, plotThresholdedFrame, and plotCandidateFrame. If would like to call these functions many times, this avoids reading the video into memory repeatedly.

## Not run: 
### many of the functions in this package are interconnected so the
### easiest way to learn to use the package is by working through the vignette,
### which is available at ajpete.com/software

#assumes you have run the example for the "scalpel" function
#read in the raw data
rawY = getY(scalpelOutput = scalpelOutput, videoType = "raw")
#read in the processed data from Step 0
processedY = getY(scalpelOutput = scalpelOutput, videoType = "processed")

## End(Not run)