Detrend F traces before neuropil fitting

Different photobleaching rates for a cell body vs neuropil ROI creates a
long-timescale linear relationship that masks the short-timescale
neuropil relationship we want to fit. Detrending both traces isolates
the short-timescale component.
Ignore nans when calculating mean images.

The meanRef and lucasKanade function used to propagate nans in one frame
to all frames when averaging. If a single frame had a large motion
correction shift and thus many nans, all those pixels would be blanked
in all averages. This commit fixes this.
Added Matthias' version of pixel covariance calculation.

This function calculates the covariance within a square neighborhood for
all pixels. The output can be used by selectROIs.
Added aux funs for Matthias.

These functions might be deleted or moved into the common code base
soon.
Added function to calculate activity overview image.

The activity overview image shows, for each pixel, the variance of the
correlation of this pixel with its neighbors. Assuming that this value
is lower for the neuropil than for active cells, this gives an overview
of where active cells are. Works with the pixCov matrix returned by
calcPxCovMJLM.
Changed selectROIs to not expect 512x512 images.
use actual size of img without assuming 512x512 image size
Fixed selectROIs mask size

Was 512x512 by default, now matches movie size
Merge remote-tracking branch 'origin/master'

Conflicts:
	@Acquisition2P/selectROIs.m
selectRois conflict resolution
Merge branch 'master' of https://github.com/HarveyLab/Acquisition2P_class
returned to default

Conflicts:
	@Acquisition2P/selectROIs.m
Revert "Fixed selectROIs mask size"

This reverts commit b1cafcbb767c2ae30881c6c67cb62aeb712e7cea.

Conflicts:
	@Acquisition2P/selectROIs.m
Merge branch 'master' of https://github.com/HarveyLab/Acquisition2P_class
New version of indexMovie. Not backwards compatible.

Indexmovie now stores data such that all frames for one pixel can be
extracted very fast. This means that traces can be loaded from disk with
minimal delay during selectCells or extractROIs. See file for details on
how to use the new format. Use the method mat2binInd to quickly convert
a linear index into an nRows-by-nCols frame into corresponding indices
into the binary movie file.
Store movie sizes during motion correction.

Movie dimensions are now stored during motion correction. Old
acquisition2p-objects lacking this information can be updated using the
addMovieSizes function.
Updated extractRois for new binary movie files.

Use extractROIsBin with binary movie files, or extractROIsTIFF for tiff
files. The old extractROIs was renamed into extractROIsOld for use with
existing binary files. This means that code still using the old bin file
will be automatically broken (no mor extractROIs function) so that the
spots that need to be updated can be found quickly.
Added aux function to calculate a nice overview image based on pixel-pixel covariance.

This image indicates which pixels belong to active cells.
Merge remote-tracking branch 'origin/master' into matthias-selectRois-dev