digitizeImages {StereoMorph}

Opens the StereoMorph Digitizing App

Description

This function opens an application in the user's default web browser for manually digitizing landmarks and Bezier curves from photographs.

Usage

	
digitizeImages(image.file, shapes.file=NULL, landmarks.file=NULL, 
     control.points.file=NULL, curve.points.file=NULL, 
     cal.file=NULL, landmarks.ref=NULL, curves.ref=NULL, image.id=NULL, 
     landmark.color.blur = 'blue', landmark.color.focus = 'green', 
     curve.color.blur = 'purple', control.point.color.blur = 'purple', 
     control.point.color.focus = 'red', landmark.radius = 4, 
     control.point.radius = 4, marker.stroke.width = 2, app.dir=NULL)

Arguments

image.file

file path to the image or images to be digitized. This can be a folder containing one or more images or a vector of file paths of one or more images.

shapes.file

file path or folder indicating where shape files should be saved. This is a new format that is currently only intended to be used when collecting 2D data. The other input types (landmarks.file, control.points.file, curve.points.file) will be phased out in future updates and replaced with this format.

landmarks.file

same input as landmarks.file in digitizeImage. Included for backward compatibility. This will eventually be phased out.

control.points.file

same input as control.points.file in digitizeImage. Included for backward compatibility. This will eventually be phased out.

curve.points.file

same input as curve.points.file in digitizeImage. Included for backward compatibility. This will eventually be phased out.

cal.file

file path to calibration file created by calibrateCameras.

landmarks.ref

landmarks to be digitized. This can either be a file path to a .txt file containing the landmarks (listed in a single column, each on a separate line) or a vector of landmark names.

curves.ref

curves to be digitized. For each curve, the name of the curve, the starting point and the ending point must be specified. curves.ref can either be a three-column matrix (with the curve name in the first column, the starting point in the second and the end point in the third) or a file path to a .txt file containing a three-column curve reference matrix. If a file path, the file should have no header and tab-separated row values.

image.id

image IDs to be saved with each image. These will be used to reference shape data in the output of readShapes. If NULL, the filenames of the images will be used (without the file extension).

landmark.color.blur

color of an unselected landmark. It might be necessary to change if the background color is close to the default. Colors must be valid SVG color names or codes (e.g. "hotpink", "#4B0082", etc.). A web-search for "SVG color codes" will indicate several possible options.

landmark.color.focus

color of a selected landmark. See landmark.color.blur.

curve.color.blur

color of digitized curves. A different color for a selected curve is not yet supported. See landmark.color.blur.

control.point.color.blur

color of an unselected control point. See landmark.color.blur.

control.point.color.focus

color of a selected control point. See landmark.color.blur.

landmark.radius

radius of digitized landmarks.

control.point.radius

radius of the Bezier control points.

marker.stroke.width

thickness of the lines used to draw the landmarks and control points.

app.dir

changes the shiny app directory for debugging.

Details

This function opens a digitizing app in the user's default browswer and allows for the digitization of landmarks and Bezier curves from photographs. Although the app runs in a web browser, the user does not have to be connected to the internet as the app runs on a local server. The R package 'shiny' handles the communication between the browser and the R console. Safari, Chrome and Opera all provide full compatibility with the apps's features. Please see StereoMorph tutorials for step-by-step tutorials on how to use StereoMorph for 2D or 3D shape data collection.

Value

NULL

Author(s)

Aaron Olsen

See Also

readShapes