Developer Documentation¶
The SIMcheck project uses Apache Maven 1 as a build and dependency
management tool. After the mvn package
phase, the SIMcheck_.jar
file
that appears in the target directory should be copied to an ImageJ plugin
folder. SIMcheck will appear in the menu after restarting the ImageJ
application.
Layout & Documentation¶
API javadocs are generated and can be found in target/apidocs
. Briefly,
the main SIMcheck_ class
produces a dialog that runs the other check
plugins. The ImageJ menu entries are defined in the plugins.config
file in src/main/resources/
, where a SIMcheck
subdirectory contains
custom Look-Up Tables. In addition to the main SIMcheck dialog and plugins that
appear in the SIMcheck menu (named starting with Raw_
for raw data checks,
Rec_
for reconstructed data checks, Cal_
for calibration checks and
Util_
for utility plugins) , there are a number of supporting classes:
DFT1D
hand-coded, multithreaded 1D Discrete Fourier Transform
FFT2D
extension of ImageJ’s FHT class, adding new methods (win func, phase..)
I1l
class containing static utility methods used throughout other classes
J
a class containing static utility methods not specific to ImageJ
OrthoReslicer
customized, stripped-down version of ImageJ’s Slicer plugin
Radial_Profile
customized version of Paul Baggethun’s Radial Profile plugin
ResultSet
a container for results (images, statistics and information strings) with code for auto-generating reports
TestData
defines paths to test data for manual
.main()
testing of plugins
Testing¶
A limited JUnit test suite is provided in src/main/test
, and most classes
define a package-private .test()
method for testing class internals
using only code-generated data. This is in contrast to the .main()
plugin
methods intended for manual testing during development, which access real data
using paths defined in the TestData
class.
- 1
Earlier versions of the project included and Ant build script and it was required, before building the project, to make a ./lib/ directory containing a soft link to the ij.jar from the desired ImageJ version, as well as a soft link to junit.jar. The built result was copied to ./plugins/ which was intended to be a soft-link this to the local ImageJ plugins folder. Typing “ant” built the default (all) target, and after restarting ImageJ or selecting Help->Refresh Menus SIMcheck would appear in the menu.