I have been developing a code that will run through a directory of images containing a specific string (DAPI, GFP). Two images with the same sub-strings will be matched to each other using these two differing sub-strings. The other sub-strings are the images name (usually what drugs were run on it) and its numerical identifier.
So far I have written a code that works perfectly in Eclipse and prints out all of the image names in the proper pairing order.
So basically the code pairs like this:
Whenever I try to run this in FIJI it requires me to save it first before running it and then I get the following error.
Started JFileChoose_Tes.txt at Tue Dec 01 12:38:17 EST 2015
java.io.FileNotFoundException: C:\Users\Stewart Lab\Desktop\Research\ImageJ Macros\JFileChoose_Tes.txt (The system cannot find the file specified)
at java.io.FileInputStream.open(Native Method)
Now I am incredibly new to development with Java let alone Maven & FIJI so I have been pouring through tutorials on it. I am just hopelessly lost on what is needed by FIJI to properly run a plugin coded in JAVA.
Everything under the “doSomething()” method will eventually just be the actions I would normally do to my images, so basically it will be a macro nested inside of the plugin. I am well able to do that, and now I have coded the other side which allows me to choose a directory and pair images, it’s just putting the two together that is holding me up now.