runmacro: Launch ImageJ shape indices macro
In jinyung/otolith: Identification of fish otolith using digital images

Description Usage Arguments Details Value Note References

This function launches ImageJ macro from shell, the macro will calculate dimensionless shape indices from otolith images.

1	runmacro(imagejdir, opendir, savedir, threshold = 30)

`imagejdir`	path to folder that contain the ImageJ's "ij.jar" file, see details
`opendir`	path to folder that contain the otolith images to be processed, see details
`savedir`	path to folder that the output files will be saved, see details.
`threshold`	numeric. threshold value to be passed to ImageJ. range within 0-255, which is different from the `img2landmark` that use a 0-1 range.

if imagejdir is not given, this function will check whether ImageJ can be launched from the ImageJ bundled within the package (only works with the installation of package-zip that bundled with ImageJ), if not, a GUI folder selector will pop out to prompt user to choose the folder to locate ImageJ. Note: when using package-zip without ImageJ bundled with, user need to put the batch_shape_indices_macro.ijm file into the "macro" folder of ImageJ or Fiji, and also put the Particle 8 plugin into the plugin folder, see ref. When opendir or savedir are not given, a GUI selector will pop out, and user can choose the folder.

For each image, a file named <image name>_shapedescriptors.txt will be generated, containing calculated shape descriptor indices

Because choose.dir() is used in the function, which is Windows specific, this function works in Windows only. User is advised to give the path of directories manually if it doesn't work. The shell command was tested under Windows only, may not work in other OS.

The Particle 8 ImageJ's plugin at G Landhini's website (http://www.mecourse.com/landinig/software/software.html)

jinyung/otolith documentation built on May 19, 2019, 10:36 a.m.