read.ijdata: Read ImageJ zip file containing several ROI files and extract...
In sclero: Measure Growth Patterns and Align Sampling Spots in Photographs

Description Usage Arguments Details Value Author(s) See Also Examples

A wrapper function, which reads an ImageJ zip file containing a collection of ROI files and outputs a list of data frames ready for convert.ijdata function.

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read.ijdata(X, spots = "point", gbs = "polyline", main = "line",
  names = "generate.invalid", spot.names = NULL, gbs.names = NULL,
  main.name = "main", sample.name = "file", scale = 1, unit = NULL)

`X`	character string defining the name (including extension) or file path of an ImageJ zip file. Alternatively an `ijzip` object.
`spots`	optional. A character argument specifying the type of ROI objects that should be considered as sample spot sequences. Alternatively a numeric vector specifying the order of elements or a character vector specifying the names of ROI objects that should be assigned as sampling spot sequences. Defaults to `"point"` (See "Details" for further information).
`gbs`	optional. A character argument, numeric vector or character vector specifying the type of ROI objects that should be considered as growth bands. Defauls to `"polyline"`. f left empty the remaining elements that are not defined in holes and main are assumed to be growth lines. For further information see `spots` and "Details". At the moment `spots` must be specified for this option to work.
`main`	optional. A character argument specifying the type of ROI object that should be considered as the measurement axis. Only one measurement axis per ImageJ .zip file is allowed. Defaults to `"line"`. At the moment `spots` must be specified for this option to work.
`names`	optional. A character argument specifying how the names of `spots` and `gbs` should be generated. These names will be used in further functions (`convert.ijdata`, `spot.dist`). In general, it is adviced to use simple ROI names without special characters (for example `-` is not allowed in a ROI name; see 'Details'). Possible `names` options are: `"generate.invalid"` (default). Uses the ROI object names, except when they are not valid `data.frame` column names. In the latter case sequential names will be generated. `"generate"`. Generates sequential names for all elements. `"keep"`. Uses the ROI object names, except when they are not valid `data.frame` column names. In the latter case `make.names` function will be used to generate `data.frame` combatible column names. `"force.keep"`. Uses the ROI object names as they are in the .zip file. Using this option might cause problems in consequent functions and is not recommended. `"manual"`. Names for both `spots` and `gbs` are searched from `spot.names` and `gbs.names` arguments, respectively. `"manual.spots"`. Names for `spots` are searched from `spot.names` argument. Names for `gbs` are generated following `"generate.invalid"`. `"manual.gbs"`. Names for `gbs` are searched from `gbs.names` argument. Names for `spots` are generated following `"generate.invalid"`.
`spot.names`	optional. A character vector of equal length to `spots` defining the names of sample spot sequences. Required if `names = "manual"` or `"manual.spots"`. Ignored otherwise.
`gbs.names`	optional. A character vector of equal length to `gbs` defining the names of growth bands. Required if `names = "manual"` or `"manual.gbs"`. Ignored otherwise.
`main.name`	optional. A character vector of lenght 1 defining the name of the measurement axis (`main`). If `main.name = "keep"`, the ROI object name will be used (not recommended, see "Details"). Otherwise the name will be taken from the argument. Defaults to `"main"`.
`sample.name`	optional. A character vector of length 1 defining the name of the sample. File name without the extension or alternatively `ijzip` object name is used as a default (`sample.name = "file"`).
`scale`	optional. A numeric value defining the scale of photograph in pixels / `unit`. Defaults to 1.
`unit`	optional. A charater vector of length 1 defining the unit of measurements. See `scale`.

In order to minimize the amount of text to be typed by a user, ROI objects of type "point" (this includes the "Multi-point Tool" points) are considered as sample spot sequences (spots) by default. Further, all "polyline" objects are assumed as growth bands (gbs) and "line" objects as the measurement axis (main) resulting to that only one "line" object is allowed per .zip file using the default settings. Alternatively, the user can specify the spots, gbs, and main objects manually using the order of the ImageJ .zip file with the exception that only one measurement axis is allowed per rawDist or spotDist object.

Punctuation characters other than _ or . should not be used as names of spots or gbs, because they tend to confuse the internal grep functions in spot.dist function. Hence it is adviced to use one of the options renaming invalid names of spots and gbs ("generate.invalid", "generate", "keep").

Returns an "IJDATA" object, which is a list of data frames containing the x and y coordinates for sampling spot sequences (spots.x and spots.y), growth bands (gbs.x and gbs.y), and measurement axis (main.x and main.y) together with sample name, scaling factor and unit of measurement.

Mikko Vihtakari

order.ijdata for ordering and subsetting read.ijdata output.

convert.ijdata for converting the coordinate information to spatstat point patterns.

spot.dist for aligning sample spot sequences.

read.ijroi and read.ijzip for reading ImageJ ROI and .zip files.

# Locate the example zip file
path <- file.path(system.file("extdata", package = "sclero"), "shellspots.zip") 

# You can replace 'path' by 'Your_file_name.zip'
dat <- read.ijdata(path) 
summary(dat)

## Works also for IJZIP objects
dat2 <- read.ijzip(path)
dat2 <- read.ijdata(dat2)
dat[!(dat %in% dat2)] # Only the sample name differs