StereoMorph (version 1.4)

digitizeImage: 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

digitizeImage(image.file, landmarks.file=NULL, control.points.file=NULL,
              curve.points.file=NULL, shapes.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

a 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.

landmarks.file

a file path indicating where the landmarks should be loaded from and/or saved to. If landmark.file is a folder, then landmark files are assumed to have the same name as the images (with a .txt extension). Alternatively, this can be a vector o

control.points.file

a file path indicating where the Bezier control points should be loaded from and/or saved to. If control.points.file is a folder, then control point files are assumed to have the same name as the images (with a .txt extension). Alternatively,

curve.points.file

a file path indicating where the Bezier curve points should be saved to. If curve.points.file is a folder, then curve point files are assumed to have the same name as the images (with a .txt extension). Alternatively, this can be a vector of

shapes.file

a 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.

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 secon

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

The 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

landmark.color.focus

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

curve.color.blur

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

control.point.color.blur

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

control.point.color.focus

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

landmark.radius

The radius of digitized landmarks.

control.point.radius

The radius of the Bezier control points.

marker.stroke.width

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

app.dir

Changes the shiny app directory for debugging.

Value

• NULL

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.

One or more images can be uploaded to the app. If more than one image is uploaded (via image.file), users can switch between images within the app by clicking the "Previous Image" and "Next Image" buttons in the app control panel. The app can be used to digitize landmarks only, curves only or both landmarks and curves. To only digitize landmarks omit the arguments control.points.file, curve.points.file and curves.ref. To only digitize curves, omit the arguments landmarks.file and landmarks.ref. If the files input via landmarks.file and control.points.file already contain landmarks or control points, these will be loaded in the app and can be modified and re-saved.

The app can save both Bezier control points and Bezier curve points. The former are the points that can be added and moved by the user while digitizing; these are used to change the shape of the curve but are not the curve points themselves. The latter are hundreds of points at single-pixel spacing that actually describe the curve and are appropriate for subsequent shape analysis. These are generated by the pointsOnBezier() function in the R package 'bezier'. While it is necessary to specify control.points.file when digitizing curves, curve.points.file is optional.

For a step-by-step tutorial on how to open and use the StereoMorph Digitizing App and download the StereoMorph Tutorial folder, see http://stereomorph.blogspot.com/2014/08/digitizing-photographs.html{Digitizing with StereoMorph}. Additional instructions can be found by clicking on 'Help' in the right upper corner of the app (or viewing the help file http://home.uchicago.edu/~aolsen/software/stereomorph/help.html{here}).

See Also

readShapes

Examples

## THE FOLLOWING EXAMPLES CAN BE RUN
## BUT USERS MUST FIRST DOWNLOAD THE STEREOMORPH TUTORIAL FOLDER
## SEE DETAILS ABOVE

## TO DIGITIZE ONLY LANDMARKS IN A SINGLE IMAGE
digitizeImage(
   image.file = "Object images/obj1_a1_v1.JPG",
   landmarks.file = "Landmarks 2D/obj1_a1_v1.txt",
   landmarks.ref = "landmarks_ref.txt")

## TO DIGITIZE ONLY LANDMARKS IN MULTIPLE IMAGES
digitizeImage(
   image.file = c("Object images/obj1_a1_v1.JPG", "Object images/obj1_a1_v1.JPG"),
   landmarks.file = c("Landmarks 2D/obj1_a1_v1.txt", "Landmarks 2D/obj1_a1_v1.txt"),
   landmarks.ref = "landmarks_ref.txt")

## OR ALTERNATIVELY, IF "OBJECT IMAGES" IS A FOLDER CONTAINING IMAGES
digitizeImage(
   image.file = "Object images",
   landmarks.file = "Landmarks 2D",
   landmarks.ref = "landmarks_ref.txt")

## DIGITIZING CURVES
digitizeImage(
   image.file = "Object images",
   control.points.file = "Control points",
   curve.points.file = "Curve points 2D",
   curves.ref = "curves_ref.txt")

## DIGITIZING LANDMARKS AND CURVES
digitizeImage(
   image.file = "Object images",
   landmarks.file = "Landmarks 2D",
   control.points.file = "Control points",
   curve.points.file = "Curve points 2D",
   landmarks.ref = "landmarks_ref.txt",
   curves.ref = "curves_ref.txt")