CurveMatch
Table of Contents
Overview
This tool is a Java application that elastically matches a collection of curves by shape and computes the mean of the collection.
Description
The user provides a collection of curves. These curves may have an arbitrary parameterization; in other words, the vertices do not need to be anatomically homologous. When the curves are generated, they typically have an irregular parameterization. A common solution is to resample the curves linearly in arclength. This does not necessarily match regions that are anatomically homologous. This tool computes a more appropriate resampling function that minimizes the difference in shape, establishing anatomically homologous vertices across the collection and computing the mean shape in the process. After resampling, the curves are ready for vertex-based statistical analysis or further processing.
Input formats
The user specifies the collection of curves as a list of filenames. The tool can read any ShapeTools-compatible file format.
Output formats
The user specifies a filename for the mean curve and a list of filenames for the matched curves. The list must be the same length as the input list. The output file format will be the same as the input shapes.
Command Line Arguments
| Argument | Type | Required | Description | Notes |
|---|
| -overwrite | flag | No | Enables file overwriting | |
| -debug | flag | No | Enables additional error reporting | |
| -input | File | Yes | Used to specify the input curve list filename | |
| -output | File | Yes | Used to specify the output curve list filename | |
| -output_mean | File | No | Used to specify the output mean curve filename | |
| -help | flag | No | Prints help and usage information. | |
| -version | flag | No | Prints version number of this application. | |
| -verbose | flag | No | Enables detailed status messages. | |
| -license | flag | No | Prints license details, and exits. | |
| -twiki | flag | No | Writes command line arguments as a TWiki format table to output and exit. | |
| -pipeline | flag | No | Write pipeline descriptor file to output and exit. | |
| -pipelineJar | String | No | Specify path to an application jar file, as a pipeline resource. | Example: "pipeline://localhost//home/zed/Connery.jar" |
| -pipelineJvm | String | No | Specify a Java Virtual Machine called by a pipeline. | |
| -pipelineJvmOptions | String | No | Specify Java Virtual Machine options used by a pipeline. | |
