choice: Alignment choice game to align internal reference planes...

In jdknguyen/SMART: SMART (Semi-manual alignment to reference template): a pipeline for whole brain mapping projects

Alignment choice game to align internal reference planes (W).

Description

User friendly way to play the wholebrain choice game to align internal reference atlas plates. Automatically saves images of chosen aligned images in the folder specified by setup$savepaths$out_reference_aligned. For use with mapping whole brain only.

Usage

choice(
  setup,
  touchup = NA,
  midpoint = FALSE,
  filetype = c("tif"),
  xpos = c(200, 760, 1350),
  brightness = 70,
  font_col = "white",
  font_size = 80,
  font_location = "+100+30",
  gravity = "southwest",
  choice_step = c(200, 100, 30, 10),
  atlas = TRUE,
  at_pos = 0
)

Arguments

setup	(required) Setup list from setup_pl().
touchup	(default = NA) Enter a vector of reference AP coordinates. The choice game will replay for just those points. Note: Numbers entered will be rounded to the nearest atlas plates. No need to enter exact atlas AP numbers.
midpoint	(default = FALSE) Play the midpoint game following choice the choice game.
filetype	(optional, default = "tif") Image format to save. Setting this argument as a vector of image formats, e.g. c("tif", "png") will save both image types. Options: common image formats like "tiff", "png", "jpeg", "gif", "rgb" or "rgba". See magick package documentation for more info on the image_write() function
xpos	(optional, default = c(200, 760, 1350)) A vector of x-positions in pixels justified to the left of the main computer screen for the three choice windows.
brightness	(optional, default = 70) Popup image brightness.
font_col	(optional, default = "white") Image annotation font color.
font_size	(optional, default = 80) Image annotation font size.
font_location	(optional, default = "+100+30") Text position from center of gravity parameter in pixels
choice_step	(optional, default= c(200,100,30,10)) Determines the successive "zoom" of images picked on either side of the center image.
atlas	(optional, default = TRUE) Will automatically pull the atlas image up during the choice game.

Value

The argument assigned to setup is returned with aligned internal z numbers matching internal AP coordinates.

jdknguyen/SMART documentation built on May 30, 2022, 10:51 p.m.