1. Variables

class PecanPie

Parameter	Data Type	Dimensions	Description
`self.read_path`	str	N/A	path to directory with data files (.npy and .bin)
`self.save_path`	str	N/A	path to directory for saving. (Default) go up one level and create a folder called "outputs"
`self.save_path_fig`	str	N/A	path to directory for saving figure outputs. (Default) create a folder called "figures" in save_path
`self.save_path_data`	str	N/A	path to directory for saving data outputs. (Default) create a folder called "data" in save_path

Parameter	Data Type	Dimensions	Description
`self.F`	ndarray	ROIs x timepoints	fluorescence traces (i.e. raw)
`self.Fneu`	ndarray	ROIs x timepoints	neuropil fluorescence traces (i.e. baseline)
`self.spks`	ndarray	ROIs x timepoints	deconvolved traces (i.e. activities)
`self.stat`	list	ROIs x 1	statistics computed for each cell
`self.ops`	dictionary	N/A	options and intermediate outputs
`self.iscell`	ndarray	ROIs x 2	specifies whether an ROI is a cell, first column is 0/1, and second column is probability that the ROI is a cell based on the default classifier
`self.bindata`	ndarray	time x Ny x Nx	registered (i.e. motion-corrected) images

Parameter	Data Type	Dimensions	Description
`self.cells_to_plot`	ndarray	N x 1	indexes to selected cells for plotting (Default) list of ROIs identified as cells in suite2p
`self.cells_to_process`	ndarray	N x 1	indexes to selected cells for data analysis (Default) list of all ROIs identified in suite2p
`self.dfof`	ndarray	ROIs x timepoints	delta F over F for all ROIs
`self.ori_metadata`	DataFrame	ROIs x properties	original metadata calculated by suite2p for all ROIs. columns include 'iscell', 'area', 'radius', 'aspect_ratio', 'compact', 'solidity', 'skip'
`self.metadata`	DataFrame	ROIs x properties	metadata of cells_to_process. columns include 'ROInum', 'iscell', 'area', 'centroid', 'major_axis', 'minor_axis', 'orientation', 'aspect_ratio', 'circularity', 'perimeter', 'compact', 'solidity'

self._im : list of dictionaries, each item in the list contains information for one canvas

Parameter	Data Type	Dimensions	Description
`'imdata'`	ndarray	Ny x Nx	image data to plot
`'line_data'`	list of dictionaries	N/A	Each item in list contains dictionary storing data of one line. Each dictionary contains the keys 'x', 'y', 'color', 'linewidth', 'visible'
`'title'`	str	N/A	figure title
`'xlabel'`	str	N/A	label of x-axis
`'ylabel'`	str	N/A	label of y-axis
`'xlim'`	list	2	[xmin, xmax]
`'ylim'`	list	2	[ymin, ymax]
`'cmap'`	str	N/A	colormap of images
`'canvas'`	int	N/A	number of the canvas to plot
`'type'`	str	N/A	type of plot, 'image', 'image & line'
`'plot'`	bool	N/A	whether to show plot or not
`'filename'`	str	N/A	filename of figure to be save

Parameter	Data Type	Dimensions	Description
`'_color'`	dict	number of defined colors	colours used in plots
`'_linewidth'`	int	N/A	linewidth used in plots
`'_tmp'`	list	N/A	for storing temporary variables
`'_verbose'`	bool	N/A	whether to print timing of processes