--- a/imagej2_analyze_particles_binary_jython_script.py	Sun Nov 05 10:47:25 2023 +0000
+++ b/imagej2_analyze_particles_binary_jython_script.py	Wed Sep 25 16:00:05 2024 +0000
@@ -1,27 +1,32 @@
 import sys
 
-from ij import IJ
+from ij import IJ, Prefs
 from ij.plugin.filter import Analyzer
 
 OPTIONS = ["edm=Overwrite", "iterations=1", "count=1"]
 
 # Fiji Jython interpreter implements Python 2.5 which does not
 # provide support for argparse.
-error_log = sys.argv[-14]
-input_file = sys.argv[-13]
-black_background = sys.argv[-12] == "yes"
-size = sys.argv[-11]
-circularity_min = float(sys.argv[-10])
-circularity_max = float(sys.argv[-9])
-show = sys.argv[-8]
-display_results = sys.argv[-7] == "yes"
-all_results = sys.argv[-6] == "yes"
+roi_coordinate_file = sys.argv[-13]
+input_file = sys.argv[-12]
+black_background = sys.argv[-11] == "yes"
+size = sys.argv[-10]
+circularity_min = float(sys.argv[-9])
+circularity_max = float(sys.argv[-8])
+show = sys.argv[-7]
+display_results = sys.argv[-6] == "yes"
 exclude_edges = sys.argv[-5] == "yes"
 include_holes = sys.argv[-4] == "yes"
 output_filename = sys.argv[-3]
 output_datatype = sys.argv[-2]
 results_path = sys.argv[-1]
 
+
+if black_background:
+    Prefs.blackBackground = True
+else:
+    Prefs.blackBackground = False
+
 # Open the input image file.
 input_image_plus = IJ.openImage(input_file)
 
@@ -42,9 +47,32 @@
     IJ.run(input_image_plus_copy, "Make Binary", "")
 
 # Set the options.
-options = ["size=%s" % size]
+options = ["size=%s" % size, "stack"]
 circularity_str = "%.3f-%.3f" % (circularity_min, circularity_max)
 options.append("circularity=%s" % circularity_str)
+if exclude_edges:
+    options.append("exclude")
+if include_holes:
+    options.append("include")
+
+# If you need the coordinates of ROIs we compute it twice
+if len(roi_coordinate_file) > 0:
+    options2 = list(options)
+    options2.append("show=Overlay")
+    IJ.run(input_image_plus_copy, "Analyze Particles...", " ".join(options2))
+    ov = input_image_plus_copy.getOverlay()
+    with open(roi_coordinate_file, 'w') as fo:
+        fo.write("shape\tpoints\tlabel\tt\tz\n")
+        for i, roi in enumerate(ov):
+            if roi.getName() is None:
+                roi.name = "ROI_%d" % i
+            poly = roi.getPolygon()
+            x_values = poly.xpoints
+            y_values = poly.ypoints
+            points_coo = ",".join(["(%d,%d)" % (x, y) for x, y in zip(x_values, y_values)])
+            fo.write("Polygon\t%s\t%s\t%d\t%d\n" % (points_coo, roi.getName(), roi.getTPosition(), roi.getZPosition()))
+    analyzer.resetCounter()
+
 if show.find("_") >= 0:
     show_str = "[%s]" % show.replace("_", " ")
 else:
@@ -52,12 +80,6 @@
 options.append("show=%s" % show_str)
 if display_results:
     options.append("display")
-    if not all_results:
-        options.append("summarize")
-if exclude_edges:
-    options.append("exclude")
-if include_holes:
-    options.append("include")
 # Always run "in_situ".
 options.append("in_situ")
 
@@ -68,6 +90,6 @@
 if len(output_filename) > 0:
     # Save the ImagePlus object as a new image.
     IJ.saveAs(input_image_plus_copy, output_datatype, output_filename)
-if display_results and len(results_path) > 0:
+if len(results_path) > 0:
     results_table = analyzer.getResultsTable()
     results_table.saveAs(results_path)