import_oufti: Import _Oufti_ data
In vicstefanou/ViSCA: Cell-Movie Analysis and Visualization

Description Usage Arguments Details Value References

Imports a .csv file generated by Oufti and converts it into a cell list containing all the cell instants of the movie.

1	import_oufti(file, pixelR)

file

A character string naming the .csv file generated by Oufti (including the suffix ".csv") from which the data is to be imported. If it does not contain an absolute path, the file name is relative to the current working directory, getwd().

NOTE: The components should be separated by "/" on Windows.

Before using this function, the user has to open the .csv file in a text editor and manually delete or comment (by adding the character "%" at the beginning) all lines of the file until the line with the "% parameter values" string.

pixelR

The pixel ratio in units of length, a non-zero positive numeric value.

Oufti treats the whole frame as a single colony.

Oufti does not export any information about either the pixels of each cell or the pixels each colony.

Oufti users importing the data with this function are excluded from using plot_col_tree, split_cell, get_cand_merge_cells, merge_cells, get_cand_mother_cells, add_branch, create_movie, create_cell_life and view_cell.

A named list with the following components:

`col_list`	`NULL`
`cell_list`	A list containing all the cell instants of the movie. Each element of the list is a named list with the following components: `cellName` is the name of the cell, a character string in the format `"c<cellId>_f<frame>"` `frame` is the ID of the frame of the cell, a non-zero positive integer number `colony` is the ID of the colony of the cell in the `frame`, equal to `1` `daughterIds` is a vector of character strings containing the `cellName` of the linked cell(s) in the next frame, or `NULL` in case no such cells exist `length` is the length of the cell in units of length, a non-zero positive numeric value `area` is the area of the cell in squared units of length, a non-zero positive numeric value `polarity` is a numeric value defining the polarity of the cell
`Nframes`	Number of frames in the movie, a non-zero positive integer value. IDs of frames are in the range `[1, Nframes]`.
`Ncols`	Number of colonies in the movie, equal to `1`. IDs of colonies are in the range `[1, Ncols]`.
`frameH`	`NULL`
`frameW`	`NULL`