Using CreateFlyWingLandmarks

Overview

CreateFlyWingLandmarks is an application that creates landmark files from a data file that describes the shape of fly wings.

Usage Summary

To run this program, you must have a java runtime environment, version 1.5 or greater.

Usage

The prototypical usage of the the program is:
java -jar CreateFlyWingLandmarks.jar data.txt outputDir

Runtime Options

CreateFlyWingLandmarks has several runtime options which control it's behavior; the following table describes these options:

Argument	Required	Default	Description	Notes
-verbose	no	off	enable verbose processing
-help	no	off	prints the usage page
-version	no	off	prints program's version
-pipeline	no	off	prints the program's pipeline descriptor
-debug	no	off	enables verbose error reporting
-overwrite	no	off	sets the program to overwrite the output file if it exists
-num	no	off	specifies the number of samples per segment to use when sampling	By default, there is one sample per landmark
-start	no	off	specifies the index of the row containing the first fly wing to process	Row indices start with 0. By default, all fly wings are processed
-end	no	off	specifies the index of the row containing the last fly wing to process	By default, all fly wings are processed

Details

CreateFlyWingLandmarks Details

This is an application that creates fly wing landmark files for David Houle's group at FSU, given their fly wing data. These landmarks are used to compute the warps between wings. The fly wing is described geometrically by a set of splines. These splines are sampled to create the landmarks. A fly wing data file has a tab-delimited line for each fly wing, which includes details of the data's collection and the control points for the splines.

All data excluding spline control points and image filenames is ignored. The splines can be sampled at a lower bound of one landmark per spline segment. The number of samples per segment can be specified by the user with a '-num anInt' flag. By default, one sample per segment is used. A single data file specifies an arbitrary number of fly wings, but the user can specify which wings should be processed. The subset of wings that are sampled is specified by a starting index and an ending index. The user can use the '-start anIndex' and '-end anIndex' flags to specify the starting and ending indices. The starting vertex must be less than the ending vertex. By default, all fly wings are processed. The index corresponds to the line of the data. The first line is index=0.

The data file encodes the image filename from which the splines were created. This filename is used to store the calculated the landmarks. The user provides an output directory, and the base name of the image filenames for each wing are used to name the landmark file. For example if the wing image was '/images/wingImage01.tif', and the output directory was '/warp/output/', then the output landmarks would be at '/warp/output/wingImage01.lm'.

There are two required arguments for the application. The first required argument is the filename of the data file. The second required argument is the directory to which the landmark data is written.

CreateFlyWingLandmarks Examples

The application's jar is name CreateFlyWingLandmarks.jar.

The data file is data.txt and it contains the following lines:

O:\species_splines\Zaprionus_ghesquierei\small\ghe1000.tif 257 46 285.5 86.5 Fiona 25_Oct_04 Mon_PM Gabon F 0.009119926 Time stamp: 1155152765159 9 ...
O:\species_splines\Zaprionus_ghesquierei\small\ghe1001.tif 267 63.5 292.5 110.5 Fiona 25_Oct_04 Mon_PM Gabon F 0.009119926 Time stamp: 1155152763337 9 ...
O:\species_splines\Zaprionus_ghesquierei\small\ghe1002.tif 258.5 45.5 284 86 Fiona 25_Oct_04 Mon_PM Gabon F 0.009119926 Time stamp: 1155152763096 9 ...
O:\species_splines\Zaprionus_ghesquierei\small\ghe1003.tif 257 43 283.5 83 Fiona 25_Oct_04 Mon_PM Gabon F 0.009119926 Time stamp: 1155152763587 9 ...

Note: the '...' is ellipsis of the control point data

The output directory will be output

Note: The use options illustrated in the following examples may be varied in actual use to suit your needs.

Simple Example

Create landmarks for all wings using the default sampling rate:

java -jar CreateFlywingLandmarks.jar data.txt output

This would create four files: 'output/ghe1000.lm','output/ghe1001.lm','output/ghe1002.lm','output/ghe1003.lm','output/ghe1003.lm'.

Complex example

Create landmarks for the first two fly wings using 5 samples per segment, overwriting any existing output files, printing messages about program status:

java -jar CreateFlywingLandmarks.jar -verbose -overwrite -start 0 -end 1 -num 5 data.txt output

This would create two files (overwriting if necessary): 'output/ghe1000.lm','output/ghe1001.lm'

Revision: 26 July 2007