ij_classifier.py

def segment_labely(ij, folder_in, segmented, processed, classifier, macro_path, N=3):
    print("INCOMPLETE IDEA - \n")
    print("  Was planning to use 'pyimagej' to import imagej,\n")
    print("and then use ij.run_plugin to operate inside python.\n")
    print("Now have found method to get macro to run so not finishing htis now.\n")
    # example code for operations we might need.
    #image = ij.io().open('sample-data/test_image.tif')
    #ij_image = ij.WindowManager.getCurrentImage()
    #ij.py.show(ij_image)
    # plugin name is not known, its probably a long dotted java class path, eg sci.java.kit.labkit .... or something.
    #ij.py.run_plugin("LabKitSegmenter")


def save_classifier_macro(folder_in, segmented, processed, classifier, macro_path, N=3):
    # Save the ij_macro to a macro script and later call this macro_command.

    # Path flop because windows slashes cause trouble.
    # this would break any escaped spaces, but I don't think there should be any.
    folder_in = folder_in.replace('\\', '/')
    segmented = segmented.replace('\\', '/')
    processed = processed.replace('\\', '/')
    classifier = classifier.replace('\\', '/')

    # When needing to test the macro in fiji, set the reusable macro to False.
    # That will hard-code the paths into the macro.
    #
    # Making the macro reusable is good to prevent issues with multiple scripts running this code.
    #
    ij_reusable_macro = True
    args = None
    if ij_reusable_macro:
        args = {
            "folder_in": folder_in,
            "segmented": segmented,
            "processed": processed,
            "classifier": classifier,
            "N": N
        }
    # WARNING: The #@ lines MUST be left aligned no matter the python indent.
    #          The #@ lines define the macro variables
    #          I think these lines need to be at the beginning of the macro
    #          Leading blank lines appear okay.
        ij_var_section = """
#@ String folder_in
#@ String segmented
#@ String processed
#@ String classifier
#@ int N
"""
    else:
        ij_var_section = """
folder_in="{folder_in}";
segmented="{segmented}";
processed="{processed}";
classifier="{classifier}";
N={N}
""".format(folder_in=folder_in, segmented=segmented, processed=processed, classifier=classifier, N=str(N))

    ij_macro = ij_var_section + '''
    File.makeDirectory(segmented);
    File.makeDirectory(processed);
    for (i = 0; i < N; i++) {
        print(folder_in+"/Region_"+i+".tif");
        open(folder_in+"/Region_"+i+".tif");
        print("seg");
        run("Segment Image With Labkit", "segmenter_file="+classifier+" use_gpu=false");
        // run("Segment Image With Labkit", "segmenter_file="+s+" input=Region_"+i+".tif use_gpu=false");
        close("Region_"+i+".tif");
        print("Images open: "+nImages);
        // selectImage(1);
        saveAs("Tiff", segmented + "/segmentation_" + i + ".tif");
        print("bin");
        run("Make Binary", "calculate black");
        print("wat");
        //run("Watershed","stack");
        print("con");
        run("Connected Components Labeling", "connectivity=6 type=[16 bits]");
        print("sav");
        saveAs("Tiff", processed + "/morpho_" + i + ".tif");
        close("*");
    }
    // this exit command doesn't always work. When using pyimagej it seems to have no effect.
    exit();
'''
    with open(macro_path, 'w') as macro_handle:
        macro_handle.write(ij_macro)

    return ij_macro, args