import_json: Import custom-made data
In vicstefanou/ViSCA: Cell-Movie Analysis and Visualization

Description Usage Arguments Details Value

Imports a .json file containing all the cell instants of the movie and another .json file containing all the colony instants of the movie.

1	import_json(file_cells, file_cols = NULL, frameH, frameW)

`file_cells, file_cols`	Character strings naming the `.json` files (including the suffix `".json"`) containing all the cell and colony instants of the movie, respectively, from which the data is to be imported. If a string does not contain an absolute path, the file name is relative to the current working directory, `getwd()`. See the Details field for information about the format of these files. When the default value `file_cols = NULL` is used, no colony list is imported. NOTE: The components should be separated by `"/"` on Windows.
`frameH`	Frame image height in pixels, a non-zero positive integer value. This argument is ignored in case `file_cols = NULL`.
`frameW`	Frame image width in pixels, a non-zero positive integer value. This argument is ignored in case `file_cols = NULL`.

The file_cols must be a JSON array of objects. Each object denotes a colony instant of the movie and should contain the following key-value pairs (otherwise an error is produced):

colName is the name of the colony instant, a character string in the format "f<frame>_c<colony>", where "<frame>" and "<colony>" is the ID of the frame and colony (in the frame) of the colony instant, respectively.
prev_colName is a JSON array of character strings containing the colName of the corresponding colony instant(s) in the previous frame. In case one such colony instant exists, it can also be a character string. For colony instants that do not have a corresponding colony instant in the previous frame, it should be equal to "f0_c0".
next_colName is a character strings containing the colName of the corresponding colony instant in the next frame. For colony instants that do not have a corresponding colony instant in the next frame, it should be equal to "f00_c0".
colImage is the mask of the box surrounding the colony instant, a JSON array of H arrays, where H is the height of the box. Each element of the array is a JSON array of W 0s and/or 1s, where W is the width of the box. 1s denote the pixels of cells and 0s the background pixels.

NOTE: This key-value pair is not necessary.
ULcorner is a JSON array of 2 non-zero integer values denoting the upper-left pixel of the box surrounding the colony instant in global (frame) coordinates. The first integer represents the row and the second the column of the pixel.

NOTE: This key-value pair is not necessary unless the key colImage is contained (an error is produced).

The file_cells must be a JSON array of objects. Each object denotes a cell instant of the movie. Key-value pair(s) denoting numeric or boolean attribute(s) should be contained in every object. The following key-value pairs are also required to be contained in every object (otherwise an error is produced):

cellName is the name of the cell, a character string in the format "<cell>_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, a non-zero positive integer number. If the whole frame is treated as a single colony, value 1 must be used for all cells.
daughterIds is a JSON array of character strings containing the cellName of the linked cell(s) in the next frame. In case one such cell exists, it can also be a character string. In case no such cells exist, it can either be NULL or omitted.
colId is a pointer to the corresponding colony instant of the cell in the file_cols, a non-zero positive integer value.

Colonies that entered the field of view at a time point and did not exist from the beginning of the movie (i.e. from the first frame) should not have tracked cells, until they merge (if this is the case) with another existing colony. This means that no object should point to such colony instants.

NOTE: This key-value pair is not necessary unless file_cols != NULL (an error is produced) and should be omitted if file_cols = NULL (a warning is produced).
pixelList is a JSON array of arrays. Each element of the array is a JSON array of 2 non-zero integer values, indicating a pixel of the cell in colony coordinates (i.e. relative to the colImage key of the colId^th object in file_cols). The first value represents the row and the second the column of the pixel.

NOTE: This key-value pair is not necessary. It should be omitted if file_cols = NULL or if objects in file_cols do not contain the key colImage (a warning is produced).

A named list with the following components:

`col_list`	A list containing all the colony instants of the movie, or `NULL` if `file_cols = NULL`. Each element of the list is a named list having as components the corresponding key-value pairs in the `file_cols`.
`cell_list`	A list containing all the cell instants of the movie. Each element of the list is a named list having as components the corresponding key-value pairs in the `file_cells`. In case the key `pixelList` is contained, `centroid` is also computed as the mean of the `pixelList` by column. `centroid` is an 1x2 matrix of non-zero numeric values denoting the centroid (geometric center) of the cell in colony coordinates (i.e. relative to the `colImage` of the `colId^th` element in the `col_list`).
`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, a non-zero positive integer value. IDs of colonies are in the range `[1, Ncols]`. This value corresponds to the number of colonies at the start of the movie.