• • Euclidean (Rigid)

• • Similarity (Rigid with Scaling)

• • Non-linear spline with basis functions:

Library

• User Guide
• Glossary

• Javadocs

Applications

• Compute Landmark Warp Application
  • This is an application that computes a variety of landmark-based warps given two landmark files.

• Apply Landmark Warp Applications
  • This is an application that applies a given warp to a given set of data. The data could simply be points, the coordinates of a shape, or an image.

• Sample Landmark Warp
  • This is an application samples a landmark warp at regular points, encoding the output to a regular discrete data object.

• Create Ucf Landmarks Application
  • This is an application that creates landmark files from Ucf contour files. The application operates on two Ucfs at a time to ensure there is a homology between the landmarks. The application resamples the contours at a constant sampling frequency that is implicitly specified by the user.

• Create Fly Wing Landmarks Application
  • This is an application that creates landmark files from a file that describes a fly wing.

• • Downloads

Linear least squares best fit

an affine transform, this preserves Collinearity between points and ratios of distances along a line

Procrustes method (3D only)

not yet defined

Dual Quaternion (3D only)

not yet defined

Generalized Procrustes method (3D only)

not yet defined

Linear least squares best fit

not yet defined

Non-linear spline

not yet defined

Elastic pde w/ linear or hyperbolic forces (non-radial basis)

not yet defined

Biharmonic equation (thin plate spline radial basis)

not yet defined

Inverse multiquadratic radial basis

not yet defined

Gaussian radial basis

not yet defined

Wendland radial basis

not yet defined

Warp Types

(list of warps, and their definitions)

• • Programmer's Guide
  • Examples^?
  • Changes
  • Landmark Warp file format specification^?
  • Landmark file format specification^?

• • Project Bug List

• • Download

Landmark Warp Applications

There are applications to create landmarks from a UCF and to compute, apply, and sample warps.

Compute Landmark Warp Application

• • User's Guide

• • Bug List

Apply Landmark Warp Applications

• • User's Guide

• • Bug List

Sample Landmark Warp

• • User's Guide

• • Bug List

Create Ucf Landmarks Application

• • User's Guide

• • Bug List

Create Fly Wing Landmarks Application

• • User's Guide

• • Bug List

Sample Landmark Warp

This is an application samples a landmark warp at regular points, encoding the output to a regular discrete data object.

Landmark Warp Library

• • Programmer's Guide v 1.0

• Types of transformations (2D and 3D unless stated otherwise):
  • Rigid
    • Procrustes method (3D only)
    • Dual Quaternion method (3D only)
    • Rigid with Scaling
  • Generalized Procrustes method (3D only)
  • Affine
    • linear least squares best fit
  • Non-linear spline
    • elastic pde w/ linear or hyperbolic forces (non-radial basis)
    • biharmonic equation (thin plate spline radial basis)
    • inverse multiquadratic radial basis
    • gaussian radial basis
    • wendland radial basis

Table of Contents

TOC: No TOC in "CCB.LandmarkWarpTools"

Summary

Types of warps

The following types of landmark warps are supported (v.1.0)

note: this list is incomplete

Thin Plate Spline

Procrustes

Generalized Procrustes

Affine

Dual Quaternion

Landmark Warp Code Examples

Apply a warp to a 2 dimensional point

A complete program that will warp a 2 dimensional point

package test.edu.ucla.loni.ccb.warp.io;

import edu.ucla.loni.ccb.warp.ILandmarkWarp;
import edu.ucla.loni.ccb.warp.LandmarkSet;
import edu.ucla.loni.ccb.warp.LandmarkSetPair;
import edu.ucla.loni.ccb.warp.basis.IBasisFunction;
import edu.ucla.loni.ccb.warp.basis.implementations.BasisThinPlate;
import edu.ucla.loni.ccb.warp.implementations.SplineWarp;
import edu.ucla.loni.ccb.warp.io.WarpIO;
import edu.ucla.loni.ccb.warp.util.LandmarkOperations;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.IOException;

public class Simple2DLandmarkWarpExample
  {
    /**
     * This demonstrates how to apply a warp to a single two dimensional point.
     * 
     * The program creates a simple warp, applies it to
     * a new point and writes the warp to disk.
     */
    public static void main(String [] args)
      {
        try {

          // Define example landmarks
          int dim = 2;
          int num = 5;
          float distance = 5;

          float[][] refData = new float[dim][num];
          float[][] targetData = new float[dim][num];

          float[] novelPoint = { .2f, 1.4f };
          float[] warpedNovelPoint = new float[dim];

          refData[0] = new float[] { 
              distance, distance, -distance, -distance,0 };
          refData[1] = new float[] { 
              distance, -distance, -distance, distance,0 };

          targetData[0] = new float[] { 
              distance, distance, -distance,-distance, distance / 2 };
          targetData[1] = new float[] { 
              distance, -distance, -distance,distance, 0 };

          // Create the landmark objects
          LandmarkSet refSet = 
            LandmarkOperations.constructFromDimNumArray(refData);
          LandmarkSet targetSet = 
            LandmarkOperations.constructFromDimNumArray(targetData);
          LandmarkSetPair landmarks = new LandmarkSetPair(refSet, targetSet);

          // Define a basis function

          IBasisFunction basis = new BasisThinPlate(dim);

          // Compute the warp

          ILandmarkWarp warp = SplineWarp.estimate(landmarks, basis);

          // Evaluate the warp (these are not used for anything here)
          warp.evaluate(novelPoint, warpedNovelPoint);
          System.out.println("Original warped novel point = [" + warpedNovelPoint[0]
              + "," + warpedNovelPoint[1] + "].");

          // Write out the warp file
          String filename = "output/warp" + WarpIO.SUFFIX;
          FileOutputStream stream = new FileOutputStream(new File(filename));
          WarpIO.write(stream, warp);

          // Read warp file
          BufferedReader reader = new BufferedReader(
              new FileReader(new File(filename)));
          ILandmarkWarp readWarp = WarpIO.read(reader);
          
          // Demonstrate that the read warp produces the same output at the novel point
          readWarp.evaluate(novelPoint, warpedNovelPoint);
          System.out.println("Read and recomputed warped novel point = [" + warpedNovelPoint[0]
              + "," + warpedNovelPoint[1] + "].");
          
        } catch (FileNotFoundException fnfe) {
          System.err.println("Cannot read file: Reason:" + fnfe.getLocalizedMessage());
        } catch (IOException ioe) {
          System.err.println("I/O problem : Reason:" + ioe.getLocalizedMessage());
        } catch (Exception e) {
          System.err.println("Warp write failed.");
        }
      }
  }

• • Landmark Warp API JavaDoc

Compute Landmark Warp Application

Apply Landmark Warp Applications

• • Project User's Guide v 1.0

• • Project User's Guide v 1.0

• FlyWingWarpExample24Apr2007.zip: Fly Wing warping code and examples

• • Landmark file format specification 1.0^?

Compute Warp Applications

This is a collection of applications that compute a warp given two landmark files. There is one application for each type of warp that is created.

• Documentation
  • Project User's Guide v 1.0^?
• Feedback
  • Project Bug List (v1.0)
• Download Links
  • Download v 1.0^?

Apply Warp Applications

This is a collection of applications that apply a given warp to a given data. The data could simply be points stored in a landmark file, the coordinates of a shape, or an image.

• Documentation
  • Project User's Guide v 1.0^?
• Feedback
  • Project Bug List (v1.0)
• Download Links
  • Download v 1.0^?

Create Ucf Landmarks Application

This is an application that creates landmark files from Ucf contour files. The application operates on two Ucfs at a time to ensure there is a homology between the landmarks. The application resamples the contours at a constant sampling frequency that is implicitly specified by the user.

• Documentation
  • Project User's Guide v 1.0
• Feedback
  • Project Bug List (v1.0)
• Download Links
  • Download v 1.0^?

Create Fly Wing Landmarks Application

This is an application that creates landmark files from a file that describes a fly wing.

• Documentation
  • Project User's Guide v 1.0
• Feedback
  • Project Bug List (v1.0)
• Download Links
  • Download v 1.0^?

Landmark Warp Tools

Libraries and applications that support various landmark based shape and image warping methods.

TOC: No TOC in "CCB.LandmarkWarpTools"

• • Glossary of project terms.