diff imagej2_analyze_particles_binary_jython_script.py @ 0:018144807556 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/imagej2_analyze_particles_binary_jython_script.py	Tue Sep 24 17:12:52 2024 +0000
@@ -0,0 +1,95 @@
+import sys
+
+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.
+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)
+
+# Create a copy of the image.
+input_image_plus_copy = input_image_plus.duplicate()
+image_processor_copy = input_image_plus_copy.getProcessor()
+analyzer = Analyzer(input_image_plus_copy)
+
+# Set binary options.
+options_list = OPTIONS
+if black_background:
+    options_list.append("black")
+options = " ".join(options_list)
+IJ.run(input_image_plus_copy, "Options...", options)
+
+if not image_processor_copy.isBinary():
+    # Convert the image to binary grayscale.
+    IJ.run(input_image_plus_copy, "Make Binary", "")
+
+# Set the options.
+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:
+    show_str = show
+options.append("show=%s" % show_str)
+if display_results:
+    options.append("display")
+# Always run "in_situ".
+options.append("in_situ")
+
+# Run the command.
+IJ.run(input_image_plus_copy, "Analyze Particles...", " ".join(options))
+
+# Save outputs.
+if len(output_filename) > 0:
+    # Save the ImagePlus object as a new image.
+    IJ.saveAs(input_image_plus_copy, output_datatype, output_filename)
+if len(results_path) > 0:
+    results_table = analyzer.getResultsTable()
+    results_table.saveAs(results_path)