I'm trying to change the existing plugin OpenComet for ImageJ. I'm not into Java, so perhaps it's an easy task.
What I'm trying to implement are the following things
run("Bio-Formats Windowless Importer", "open=path autoscale color_mode=Default view=Hyperstack stack_order=XYCZT");
opening my files with the help of the Bioformat Importer plugin
run("Flip Horizontally");
This is supposed to be placed into the following code:
// Iterate over each input file
for(int i=0;i<inFiles.length;i++){
// Try to open file as image
//NUMBER 1 BIOFORMAT IMPORT AT THIS POINT
ImagePlus imp = IJ.openImage(inFiles[i].getPath());
// If image could be opened, run comet analysis
if(imp!=null){
//NUMBER 2 FLIPPING AT THIS POINT
String imageKey = inFiles[i].getName();
Moreover I would need to import the class of the BioFormat Importer or something like this. Wouldn't I?
Thanks a lot in advance.
run("Bio-Formats Windowless Importer", "open=path autoscale color_mode=Default view=Hyperstack stack_order=XYCZT");
opening my files with the help of the Bioformat Importer plugin
You can achieve this using the BF
helper class of bio-formats (see its API documentation). For a javascript example, have a look here. In Java, this could look like:
import loci.plugins.BF;
[...]
ImagePlus[] imps = BF.openImagePlus(inFiles[i].getPath());
ImagePlus imp = imps[0];
run("Flip Horizontally");
Use the recorder (Plugins > Macros > Record...) in Java mode to get the required command:
import ij.IJ;
[...]
IJ.run(imp, "Flip Horizontally", "");
If you want to know the Java command at a lower level, use the Command Finder (press [L] or Plugins > Utilities > Find Commands...) and type "flip" and you'll find the class that implements the command:
ij.plugin.filter.Transformer("fliph")
Hope that helps.