StereoMorph

Thursday, November 30, 2017

v1.6: New video tools added to StereoMorph

StereoMorph version 1.6 is now available on CRAN! It actually first became available back in March of this year...but I have been busy and fallen behind on updates - my sincerest apologies! With version 1.6 I have started to incorporate features to make it easier to use StereoMorph with video, particularly from GoPro cameras. This came about through a collaborative project just published this past summer with Caine Delacy, Mark Bond, and others in which we used StereoMorph to collect 3D length data from free-swimming oceanic whitetip sharks. It was a fantastic collaboration and I'm very grateful to Caine for reaching out to include me in the study. You can find our paper here!

Identifying landmarks in a frame from a GoPro video of a free-swimming oceanic whitetip shark. StereoMorph v1.6.1 includes functions to extract video frames and use these to calibrate video cameras for 3D measurements of moving objects.

Here are the key updates with version 1.6:

Video frame extraction, particularly .mov files
The ability to extract and rename frames at different portions of a video, for synchronization
A web-based tutorial guide (formerly available as a PDF).

I have edited previous posts of this blog to point users to the new corresponding tutorial webpages. I want to make sure anyone that ends up on this site has access to the most up-to-date instructions. From now on I will use this site to announce StereoMorph updates and answer user questions (using the comments below). I'll use my github site to host tutorial pages so that I can keep them updated.

Wednesday, March 16, 2016

v1.5: New tutorial and updates to digitizing app, stereo calibration, and reconstruction

StereoMorph version 1.5 is now available on CRAN! Version 1.5 comes with a brand new PDF tutorial (3 MB), example project (download; 18 MB), and includes several major updates to streamline the stereo digitization and reconstruction workflow and improve function performance. The tutorial steps laid out in early posts to this blog have been updated in the new tutorial so please refer to the new tutorial linked above. This version should also be entirely back compatible with previous versions; most of the new features are available as new functions.

New drop-down navigation and 'settings' options in StereoMorph v1.5

General updates in v1.5:

Faster and more robust checkerboard corner detection
Shortcuts to facilitate manual digitization of consecutive video frames
New digitizing interface with a dropdown menu to easily move among photographs
Improved cross-browser compatibility

Updates in v1.5 for stereo digitizing and reconstruction:

New digitizing interface that allows easy navigation among different aspects and views
The ability to project the epipolar line in the digitizing app
Faster and more robust curve reconstruction
A simpler workflow overall
A single function (calibrateCameras) for stereo camera calibration, including checkerboard corner detection and error assessment
A single function (digitizeImages) for digitizing stereo image sets, including multiple specimens
A single function (reconstructStereoSets) that reconstructs landmarks and curves, places a specified number of evenly spaced points on each curve, and unifies landmarks/curves
A single function (reflectMissingShapes) to reflect missing bilateral landmarks/curves in a series of shape sets
A single function (alignShapesToMidline) to align a set or sets of bilateral landmarks/curves to the midline plane
A single function (testCalibration) to test stereo calibration accuracy

Many thanks to the community for your feedback! Comments/questions/complaints welcome!

Wednesday, April 8, 2015

v1.4: Updates to Digitizing Application, Scaling for 2D morphometrics

StereoMorph version 1.4 just became available today on CRAN! I've made several improvements to the digitizing application based on user suggestions, particularly for 2D morphometrics.

New options in the 'Settings' panel in StereoMorph v1.4.

Users can now copy landmarks and curves from the current image to the next one, which makes it easier to digitize consecutive image frames from a video. Users can apply scaling directly in the app by digitizing points on a ruler or having the app automatically detect a checkerboard.

New 'Scaling' panel available in StereoMorph v1.4

Lastly, all of the shape and scaling data for an image can now be saved in a single text file and read into R using a single function (readShapes).

To demonstrate how to use the app, including these new features, I've made a new tutorial using different coffee mugs as an example. The tutorial is available as a PDF and you can download the example folder here (300KB).

The next updates will be to streamline 3D data collection using this same single file format. This should reduce the number of different folders that have to be created.