I’m new to development using ImageJ and a plugin called fairSIM. I am having some difficulties just getting started with it, and I was hoping someone here could get me started more quickly.
I’m using an up-to-date Arch Linux system using Java 1.8.0_92 and ImageJ 1.51d, and here are the exact steps for reproducing the issues I’m facing.
mkdir -p ~/test; cd ~/test; git clone https://github.com/fairSIM/fairSIM.git; cd fairSIM; make;
That makes a directory/folder called test in my home directory. It checks out the latest git release, goes into the directory with the Makefile (see the default Makefile here), and runs make.
Problem: The result of that is a compilation error because the Makefile bizarrely expects a program called javac6 to compile the code instead of just javac.
Solution: So, after a minor change of the Makefile by replacing javac6 with javac (the Java compiler executable), I ran make again.
Problem: This time, it tries to compile, but I got a bunch of errors related to ImageJ packages not being found.
Solution: So, I copied the ImageJ JAR file (ij.jar) into ~/test/fairSIM/ (via
cp /usr/share/imagej/ij.jar ~/test/fairSIM/ij.jar) and modified the classpath of the Makefile with
JFLAGS+= -cp ~/test/fairSIM/ij.jar (see amended Makefile).
Problem: Then, I re-ran make. This time, I encountered many fewer errors (see here). I don’t know how to get rid of these. Any advice?
Problem: I decided to ignore these errors and create a JAR anyway by running
cd ~/test/fairSIM/; make jar
The result is this. So, I still get an error. How can I fix this error?
Problem: I decided to use the resulting
fairSIM_plugin_f69908170c.jar file as a plugin with the imagej I had installed on my system through my software package manager (the usual way of installing stuff on Linux). I ran
imagej and clicked
Plugins > Install... which prompted a file chooser menu. I selected
~/test/fairSIM/fairSIM_plugin_f69908170c.jar. Imagej then gave me another file chooser menu to specify where to save this plugin (bit bizarre architecture to me to do this). So, I specified
~/.imagej/plugins/ as the directory/folder to save
fairSIM_plugin_f69908170c.jar into. This was already the default. I hit
Save and navigated to
Plugins > fairSIM > new reconstruction but ImageJ gave me an error.
Plugin or class not found: "org.fairsim.fiji.FairSIM_ImageJplugin" (java.lang.ClassNotFoundException: org.fairsim.fiji.FairSIM_ImageJplugin)
This is critically important to me that this gets resolved. What must I do to fix this?
Solution: This isn’t a real solution, but just a demonstration of what works and what doesn’t. Using a fresh, clean installation of ImageJ, I downloaded the fairSIM plugin JAR file from the fairSIM website (see here). That works perfectly fine. But, since I want to modify the code and use a modified fairSIM plugin, this won’t be an acceptable “solution.” I hope someone here can help me out!
Thanks in advance!